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Conserved domains on  [gi|1168468|sp|P43138|]
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RecName: Full=DNA repair nuclease/redox regulator APEX1; AltName: Full=APEX nuclease; Short=APEN; AltName: Full=Apurinic-apyrimidinic endonuclease 1; Short=AP endonuclease 1; AltName: Full=Redox factor-1; Short=REF-1; Contains: RecName: Full=DNA repair nuclease/redox regulator APEX1, mitochondrial

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 61-315 4.75e-162

Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


:

Pssm-ID: 197321 [Multi-domain]  Cd Length: 253  Bit Score: 451.62  E-value: 4.75e-162
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   61 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSApSDKEGYSGVGLLSRQCPLK 140
Cdd:cd09087   1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGYHQYWNA-AEKKGYSGTAILSKKKPLS 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEIDLR 220
Cdd:cd09087  80 VTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLA 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  221 NPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 300
Cdd:cd09087 160 NPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIR 238

                       250
                ....*....|....*
gi 1168468  301 SKALGSDHCPITLYL 315
Cdd:cd09087 239 SDIMGSDHCPIGLEL 253
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 61-315 4.75e-162

Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197321 [Multi-domain]  Cd Length: 253  Bit Score: 451.62  E-value: 4.75e-162
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   61 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSApSDKEGYSGVGLLSRQCPLK 140
Cdd:cd09087   1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGYHQYWNA-AEKKGYSGTAILSKKKPLS 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEIDLR 220
Cdd:cd09087  80 VTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLA 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  221 NPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 300
Cdd:cd09087 160 NPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIR 238

                       250
                ....*....|....*
gi 1168468  301 SKALGSDHCPITLYL 315
Cdd:cd09087 239 SDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 61-316 9.15e-143

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 402.81  E-value: 9.15e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468     61 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSApsdKEGYSGVGLLSRQCPLK 140
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGA---KKGYSGVAILSKVEPLD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468    141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAG-RGLVRLEYR-QRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEID 218
Cdd:TIGR00633  78 VRYGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKlQFWDALFQYLEKELDAGKPVVICGDMNVAHTEID 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468    219 LRNPKGNKKNAGFTPQERQGFGEMLQAVpLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 298
Cdd:TIGR00633 158 LGNPKENKGNAGFTPEEREWFDELLEAG-FVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSY 236

                         250
                  ....*....|....*...
gi 1168468    299 IRSKALGSDHCPITLYLA 316
Cdd:TIGR00633 237 IDSEIRGSDHCPIVLELD 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
61-316 2.55e-114

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 330.89  E-value: 2.55e-114
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   61 LKICSWNVDGLRAwIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLtHQYWSapsDKEGYSGVGLLSRQCPLK 140
Cdd:COG0708   1 MKIASWNVNGIRA-RLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGY-HVYFH---GQKGYNGVAILSRLPPED 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAG-RGLVRLEYRQRWDEAFRKFLKDL-ASRKPLVLCGDLNVAHEEID 218
Cdd:COG0708  76 VRRGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELlAPGRPLILCGDFNIAPTEID 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  219 LRNPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 298
Cdd:COG0708 156 VKNPKANLKNAGFLPEERAWFDRLLEL-GLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAG 234

                       250       260
                ....*....|....*....|..
gi 1168468  299 I----RSKALGSDHCPITLYLA 316
Cdd:COG0708 235 IdrepRGDERPSDHAPVVVELD 256
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 61-315 3.35e-88

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 264.25  E-value: 3.35e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468    61 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELpgltHQYWSApSDKEGYSGVGLLSRQCPLK 140
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGY----FDFWNC-AIKKGYSGVVTFTKKEPLS 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEIDLR 220
Cdd:PRK13911  76 VSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   221 NPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 300
Cdd:PRK13911 156 NPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIY 234

                        250
                 ....*....|....*
gi 1168468   301 SKALGSDHCPITLYL 315
Cdd:PRK13911 235 KDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 64-212 1.94e-21

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 89.59  E-value: 1.94e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468     64 CSWNVDGLRAWIKKKG------LDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSaPSDKEGYSGVGLLSRQC 137
Cdd:pfam03372   1 LTWNVNGGNADAAGDDrkldalAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGG-PGGGGGGGGVAILSRYP 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1168468    138 PLKVSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLKDLASRKPLVLCGDLNV 212
Cdd:pfam03372  80 LSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDeQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 61-315 4.75e-162

Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197321 [Multi-domain]  Cd Length: 253  Bit Score: 451.62  E-value: 4.75e-162
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   61 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSApSDKEGYSGVGLLSRQCPLK 140
Cdd:cd09087   1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGYHQYWNA-AEKKGYSGTAILSKKKPLS 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEIDLR 220
Cdd:cd09087  80 VTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLA 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  221 NPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 300
Cdd:cd09087 160 NPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIR 238

                       250
                ....*....|....*
gi 1168468  301 SKALGSDHCPITLYL 315
Cdd:cd09087 239 SDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 61-316 9.15e-143

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 402.81  E-value: 9.15e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468     61 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSApsdKEGYSGVGLLSRQCPLK 140
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGA---KKGYSGVAILSKVEPLD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468    141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAG-RGLVRLEYR-QRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEID 218
Cdd:TIGR00633  78 VRYGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKlQFWDALFQYLEKELDAGKPVVICGDMNVAHTEID 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468    219 LRNPKGNKKNAGFTPQERQGFGEMLQAVpLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 298
Cdd:TIGR00633 158 LGNPKENKGNAGFTPEEREWFDELLEAG-FVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSY 236

                         250
                  ....*....|....*...
gi 1168468    299 IRSKALGSDHCPITLYLA 316
Cdd:TIGR00633 237 IDSEIRGSDHCPIVLELD 254
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 62-315 4.81e-139

Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197307 [Multi-domain]  Cd Length: 251  Bit Score: 393.19  E-value: 4.81e-139
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   62 KICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLtHQYWSaPSDKEGYSGVGLLSRQCPLKV 141
Cdd:cd09073   1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGY-HSYWS-PARKKGYSGVATLSKEEPLDV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  142 SYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDLASR-KPLVLCGDLNVAHEEIDLR 220
Cdd:cd09073  79 SYGIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRgKPVVICGDFNVAHEEIDLA 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  221 NPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNtAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 300
Cdd:cd09073 159 RPKKNEKNAGFTPEERAWFDKLLSL-GYVDTFRHFHPE-PGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGIL 236

                       250
                ....*....|....*
gi 1168468  301 SKALGSDHCPITLYL 315
Cdd:cd09073 237 SKVKGSDHAPVTLEL 251
XthA COG0708
Exonuclease III [Replication, recombination and repair];
61-316 2.55e-114

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 330.89  E-value: 2.55e-114
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   61 LKICSWNVDGLRAwIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLtHQYWSapsDKEGYSGVGLLSRQCPLK 140
Cdd:COG0708   1 MKIASWNVNGIRA-RLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGY-HVYFH---GQKGYNGVAILSRLPPED 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAG-RGLVRLEYRQRWDEAFRKFLKDL-ASRKPLVLCGDLNVAHEEID 218
Cdd:COG0708  76 VRRGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELlAPGRPLILCGDFNIAPTEID 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  219 LRNPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 298
Cdd:COG0708 156 VKNPKANLKNAGFLPEERAWFDRLLEL-GLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAG 234

                       250       260
                ....*....|....*....|..
gi 1168468  299 I----RSKALGSDHCPITLYLA 316
Cdd:COG0708 235 IdrepRGDERPSDHAPVVVELD 256
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 61-315 9.50e-102

Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.


Pssm-ID: 197319 [Multi-domain]  Cd Length: 252  Bit Score: 298.81  E-value: 9.50e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   61 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLtHQYWSaPSDKEGYSGVGLLSRQCPLK 140
Cdd:cd09085   1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGY-HSYFN-SAERKGYSGVALYSKIEPDS 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDL-ASRKPLVLCGDLNVAHEEIDL 219
Cdd:cd09085  79 VREGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELrDSGKNVIICGDFNTAHKEIDL 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  220 RNPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYaYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKI 299
Cdd:cd09085 159 ARPKENEKVSGFLPEERAWMDKFIEN-GYVDTFRMFNKEPGQ-YTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGI 236

                       250
                ....*....|....*.
gi 1168468  300 RSKALGSDHCPITLYL 315
Cdd:cd09085 237 LPDVMGSDHCPVSLEL 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 61-313 2.09e-99

exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272954 [Multi-domain]  Cd Length: 254  Bit Score: 292.75  E-value: 2.09e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468     61 LKICSWNVDGLRAwIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLtHQYWSApsdKEGYSGVGLLSRQCPLK 140
Cdd:TIGR00195   1 MKIISWNVNGLRA-RPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGY-HVFFSG---QKGYSGVAIFSKEEPIS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468    141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGR-GLVRLEYRQRWDEAFRKFLKDLA-SRKPLVLCGDLNVAHEEID 218
Cdd:TIGR00195  76 VRRGFGVEEEDAEGRIIMAEFDSFLVINGYFPNGSRdDSEKLPYKLQWLEALQNYLEKLVdKDKPVLICGDMNIAPTEID 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468    219 LRNPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYaYTFWTYMMNARSKNVGWRLDYFLLSHSL----LPAL 294
Cdd:TIGR00195 156 LHIPDENRNHTGFLPEEREWLDRLLEA-GLVDTFRKFNPDEGA-YSWWDYRTKARDRNRGWRIDYFLVSEPLkercVDCG 233

                         250
                  ....*....|....*....
gi 1168468    295 CDSKIRSKALGSDHCPITL 313
Cdd:TIGR00195 234 IDYDIRGSEKPSDHCPVVL 252
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 61-315 3.35e-88

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 264.25  E-value: 3.35e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468    61 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELpgltHQYWSApSDKEGYSGVGLLSRQCPLK 140
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGY----FDFWNC-AIKKGYSGVVTFTKKEPLS 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEIDLR 220
Cdd:PRK13911  76 VSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   221 NPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 300
Cdd:PRK13911 156 NPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIY 234

                        250
                 ....*....|....*
gi 1168468   301 SKALGSDHCPITLYL 315
Cdd:PRK13911 235 KDILGSDHCPVGLEL 249
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 61-313 5.40e-83

Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.


Pssm-ID: 197336 [Multi-domain]  Cd Length: 253  Bit Score: 250.99  E-value: 5.40e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   61 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLtHQYWsAPSDKEGYSGVGLLSRQCPLK 140
Cdd:cd10281   1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGY-NAYF-FDAEKKGYAGVAIYSRTQPKA 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  141 VSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDL-ASRKPLVLCGDLNVAHEEIDL 219
Cdd:cd10281  79 VIYGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELrRKRREFIVCGDFNIAHTEIDI 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  220 RNPKGNKKNAGFTPQERQGFGEMLQAVPLADSFRHLYPNtAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKI 299
Cdd:cd10281 159 KNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD-EGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWI 237

                       250
                ....*....|....
gi 1168468  300 RSKALGSDHCPITL 313
Cdd:cd10281 238 YREERFSDHAPLIV 251
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 61-311 3.34e-73

Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and 3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197320 [Multi-domain]  Cd Length: 254  Bit Score: 226.24  E-value: 3.34e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   61 LKICSWNVDGLRAwikKKG--LDWVKEEAPDILCLQETKCSENKLPAE-LQELpGLtHQYWSApsdKEGYSGVGLLSRQC 137
Cdd:cd09086   1 MKIATWNVNSIRA---RLEqvLDWLKEEDPDVLCLQETKVEDDQFPADaFEAL-GY-HVAVHG---QKAYNGVAILSRLP 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  138 PLKVSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAG-RGLVRLEYRQRWDEAFRKFLKDLASR-KPLVLCGDLNVAHE 215
Cdd:cd09086  73 LEDVRTGFPGDPDDDQARLIAARVGGVRVINLYVPNGGdIGSPKFAYKLDWLDRLIRYLQKLLKPdDPLVLVGDFNIAPE 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  216 EIDLRNPKGNKKNAGFTPQERQGFGEMLQAvPLADSFRHLYPNTAYaYTFWTYMMNARSKNVGWRLDYFLLSHSLLPAL- 294
Cdd:cd09086 153 DIDVWDPKQLLGKVLFTPEEREALRALLDL-GFVDAFRALHPDEKL-FTWWDYRAGAFERNRGLRIDHILASPALADRLk 230

                       250       260
                ....*....|....*....|
gi 1168468  295 -C--DSKIRSKALGSDHCPI 311
Cdd:cd09086 231 dVgiDREPRGWEKPSDHAPV 250
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 63-315 9.56e-71

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


Pssm-ID: 197306 [Multi-domain]  Cd Length: 241  Bit Score: 219.28  E-value: 9.56e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   63 ICSWNVDGLRA-WIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSAPSDKEGYSGVGLLSRQC---P 138
Cdd:cd08372   1 VASYNVNGLNAaTRASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSGPSRKEGYEGVAILSKTPkfkI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  139 LKVSYGIGEEEHDQEGRVIVAEFES----FILVTAYVPNAGRglvRLEYRQRWDEAFRKFLKDLA--SRKPLVLCGDLNV 212
Cdd:cd08372  81 VEKHQYKFGEGDSGERRAVVVKFDVhdkeLCVVNAHLQAGGT---RADVRDAQLKEVLEFLKRLRqpNSAPVVICGDFNV 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  213 AHEEIDLRNPkgnkknagftpqerQGFGEMLQAVPLADSFRHLypntAYAYTFWTYMmnarsKNVGWRLDYFLLSHSLLP 292
Cdd:cd08372 158 RPSEVDSENP--------------SSMLRLFVALNLVDSFETL----PHAYTFDTYM-----HNVKSRLDYIFVSKSLLP 214

                       250       260
                ....*....|....*....|....*..
gi 1168468  293 ALCDSKIRSKA----LGSDHCPITLYL 315
Cdd:cd08372 215 SVKSSKILSDAararIPSDHYPIEVTL 241
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 62-311 7.81e-49

Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197322 [Multi-domain]  Cd Length: 309  Bit Score: 165.18  E-value: 7.81e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   62 KICSWNVDGLRA------WIKKKGLDWVKEE-APDILCLQETKCSENKLPAELQELPGLtHQYWSAPSDKEGYSGV---- 130
Cdd:cd09088   1 RIVTWNVNGIRTrlqyqpWNKENSLKSFLDSlDADIICLQETKLTRDELDEPSAIVEGY-DSFFSFSRGRKGYSGVatyc 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  131 ------------GLLSRQCPLKVSYGIGEE-------------------EHDQEGRVIVAEFESFILVTAYVPNAGRG-L 178
Cdd:cd09088  80 rdsaatpvaaeeGLTGVLSSPNQKNELSENddigcygemleftdskellELDSEGRCVLTDHGTFVLINVYCPRADPEkE 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  179 VRLEYRQRWDEAFRKFLKDL-ASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQG------------FGEMLQA 245
Cdd:cd09088 160 ERLEFKLDFYRLLEERVEALlKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDNPSrqwldqllgdsgEGGGSPG 239

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1168468  246 VPLADSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPI 311
Cdd:cd09088 240 GLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPV 305
PRK11756 PRK11756
exonuclease III; Provisional
 61-311 1.30e-28

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 110.75  E-value: 1.30e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468    61 LKICSWNVDGLRAwiKKKGLDWVKEE-APDILCLQETKCSENKLPAELQELPGLtHQYWSApsdKEGYSGVGLLSRQCPL 139
Cdd:PRK11756   1 MKFVSFNINGLRA--RPHQLEAIIEKhQPDVIGLQETKVHDEMFPLEEVEALGY-HVFYHG---QKGHYGVALLSKQTPI 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   140 KVSYGIGEEEHDQEGRVIVAEFESFI-LVT---AYVPNAgrglvrlEYRQRWD--EAFRKFLKDL--------ASRKPLV 205
Cdd:PRK11756  75 AVRKGFPTDDEEAQRRIIMATIPTPNgNLTvinGYFPQG-------ESRDHPTkfPAKRQFYQDLqnyletelSPDNPLL 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   206 LCGDLNVAHEEIDLRNPKGNKK------NAGFTPQERQGFgEMLQAVPLADSFRHLYPNTAYAYTFWTYmmnaRSK---- 275
Cdd:PRK11756 148 IMGDMNISPTDLDIGIGEENRKrwlrtgKCSFLPEEREWL-DRLMDWGLVDTFRQLNPDVNDRFSWFDY----RSKgfdd 222

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 1168468   276 NVGWRLDYFLLSHSLLPALCDS----KIRSKALGSDHCPI 311
Cdd:PRK11756 223 NRGLRIDLILATQPLAERCVETgidyDIRGMEKPSDHAPI 262
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 63-313 2.96e-28

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 109.36  E-value: 2.96e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   63 ICSWNVDGLRAWIKKKGL-DWVKEEAPDILCLQETKCSENKlpaELQELPGLTHQYWSApSDKEGYSGVG-LLSRQCPLK 140
Cdd:cd09076   1 IGTLNVRGLRSPGKRAQLlEELKRKKLDILGLQETHWTGEG---ELKKKREGGTILYSG-SDSGKSRGVAiLLSKTAANK 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  141 -VSYgigeeEHDQEGRVIVAEFE----SFILVTAYVPNAGRGLVRLEYRQRwdeaFRKFLKDLASRKPLVLCGDLN---- 211
Cdd:cd09076  77 lLEY-----TKVVSGRIIMVRFKikgkRLTIINVYAPTARDEEEKEEFYDQ----LQDVLDKVPRHDTLIIGGDFNavlg 147

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  212 ---VAHEEIDLRNPKGNKKNAGFTPQERqgfgemlqavpLADSFRHLYPNTaYAYTFwtymmNARSKNVGWRLDYFLLSH 288
Cdd:cd09076 148 pkdDGRKGLDKRNENGERALSALIEEHD-----------LVDVWRENNPKT-REYTW-----RSPDHGSRSRIDRILVSK 210

                       250       260
                ....*....|....*....|....*
gi 1168468  289 SLLPALCDSKIrSKALGSDHCPITL 313
Cdd:cd09076 211 RLRVKVKKTKI-TPGAGSDHRLVTL 234
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 64-212 1.94e-21

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 89.59  E-value: 1.94e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468     64 CSWNVDGLRAWIKKKG------LDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSaPSDKEGYSGVGLLSRQC 137
Cdd:pfam03372   1 LTWNVNGGNADAAGDDrkldalAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGG-PGGGGGGGGVAILSRYP 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1168468    138 PLKVSYGIGEEEHDQEGRVIVAEFESFILVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLKDLASRKPLVLCGDLNV 212
Cdd:pfam03372  80 LSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDeQRADLLLLLLALLAPRSEPVILAGDFNA 155
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 65-315 3.36e-11

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 62.31  E-value: 3.36e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   65 SWNVDGLR----AWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQEL-PGLTHqYWSAPSDKEGYSGVGLLSRQcPL 139
Cdd:cd09084   3 SYNVRSFNrykwKDDPDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLlKGYPY-YYVVYKSDSGGTGLAIFSKY-PI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  140 KVSYGIgeEEHDQEGRVIVAE--------------FESFIL----VTAYVPNAGRGLVRLEYRQRWDEAFRK-------F 194
Cdd:cd09084  81 LNSGSI--DFPNTNNNAIFADirvggdtirvynvhLESFRItpsdKELYKEEKKAKELSRNLLRKLAEAFKRraaqadlL 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  195 LKDLA-SRKPLVLCGDLN-----VAHEEIdlrnpKGNKKNAgFtpqERQGFGemlqavpladsfrhlypntaYAYTFWTY 268
Cdd:cd09084 159 AADIAaSPYPVIVCGDFNdtpasYVYRTL-----KKGLTDA-F---VEAGSG--------------------FGYTFNGL 209

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*....
gi 1168468  269 MMnarsknvGWRLDYFLLSHSL--LPALCDSKIrskalGSDHCPITLYL 315
Cdd:cd09084 210 FF-------PLRIDYILTSKGFkvLRYRVDPGK-----YSDHYPIVATL 246
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 47-311 1.28e-10

Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only];


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 61.16  E-value: 1.28e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   47 PPDQKTSASGkSATLKICSWNVdglraWIKKKG----LDWVKEEAPDILCLQETKcsenklPAELQELPGLTHQY-WSAP 121
Cdd:COG3021  82 LPAPKSAPAG-GPDLRVLTANV-----LFGNADaealAALVREEDPDVLVLQETT------PAWEEALAALEADYpYRVL 149

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  122 SDKEGYSGVGLLSRQcPLkvsygigeeeHDQEGRVIVAEFESFILVTAYVPNagrGLVRL---------EYRQRWDEAFR 192
Cdd:COG3021 150 CPLDNAYGMALLSRL-PL----------TEAEVVYLVGDDIPSIRATVELPG---GPVRLvavhpappvGGSAERDAELA 215

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  193 KFLKDLASRK-PLVLCGDLN-VAH--------EEIDLRNPkgnkknagftpqeRQGFGemlqavpladsfrhLYPntaya 262
Cdd:COG3021 216 ALAKAVAALDgPVIVAGDFNaTPWsptlrrllRASGLRDA-------------RAGRG--------------LGP----- 263

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*....
gi 1168468  263 yTFwtymmNARSKNVGWRLDYFLLSHSLLPALCDskiRSKALGSDHCPI 311
Cdd:COG3021 264 -TW-----PANLPFLRLPIDHVLVSRGLTVVDVR---VLPVIGSDHRPL 303
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 54-218 6.31e-08

Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only];


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 51.45  E-value: 6.31e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468   54 ASGKSATLKICSWNVDGLRAWIKKKGLD----WVKEEAPDILCLQEtkcsenklpaelqelpglthqywsapsdkegysg 129
Cdd:COG3568   1 AAAAAATLRVMTYNIRYGLGTDGRADLEriarVIRALDPDVVALQE---------------------------------- 46

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168468  130 VGLLSRQcPLKVSYGIGEEEHDQEGR-VIVAEFE----SFILVTAYVpnagrGLVRLEYRQRWDEAFRKFLKDLASRKPL 204
Cdd:COG3568  47 NAILSRY-PIVSSGTFDLPDPGGEPRgALWADVDvpgkPLRVVNTHL-----DLRSAAARRRQARALAELLAELPAGAPV 120

                       170
                ....*....|....
gi 1168468  205 VLCGDLNvaheEID 218
Cdd:COG3568 121 ILAGDFN----DID 130
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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