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Conserved domains on  [gi|767943466|ref|XP_011534381|]
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sphingomyelin phosphodiesterase 2 isoform X1 [Homo sapiens]

Protein Classification

exonuclease/endonuclease/phosphatase family protein( domain architecture ID 662)

exonuclease/endonuclease/phosphatase (EEP) family protein may cleave phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 6-174 2.07e-11

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.


The actual alignment was detected with superfamily member cd09079:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 259  Bit Score: 63.05  E-value: 2.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466   6 DWFSGKAVGLlVLHLSGMVLNAYVTHLHAEYNrqkdiylaHRVAQAWELAQFIHHTSKKADVVLLCGDLNMHP----EDL 81
Cdd:cd09079  113 DYKSRKILGA-TIEINGQPIDVYSCHLGWWYD--------EEEPFAYEWSKLEKALAEAGRPVLLMGDFNNPAgsrgEGY 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  82 GCCLLKEWTGLHDAYLETRDfkgseeGNTmVPKNcyVSQQElkPFPFGVRIDYVLYKAvsgfYISCKSFETTtgFDPHRG 161
Cdd:cd09079  184 DLISSLGLQDTYDLAEEKDG------GVT-VEKA--IDGWR--GNKEAKRIDYIFVNR----KVKVKSSRVI--FNGKNP 246

                        170
                 ....*....|...
gi 767943466 162 TPLSDHEALMATL 174
Cdd:cd09079  247 PIVSDHFGVEVEL 259
 
Name Accession Description Interval E-value
RgfB-like cd09079
Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, ...
 6-174 2.07e-11

Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, and related proteins; This family includes Streptococcus agalactiae RgfB (for regulator of fibrinogen binding) and related proteins. The function of RgfB is unknown. It is part of a putative two component signal transduction system designated rgfBDAC (the rgf locus was identified in a screen for mutants of Streptococcus agalactiae with altered binding to fibrinogen). RgfA,-C,and -D do not belong to this superfamily: rgfA encodes a putative response regulator, and rgfC, a putative histidine kinase. All four genes are co-transcribed, and may be involved in regulating expression of bacterial cell surface components. 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: 197313 [Multi-domain]  Cd Length: 259  Bit Score: 63.05  E-value: 2.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466   6 DWFSGKAVGLlVLHLSGMVLNAYVTHLHAEYNrqkdiylaHRVAQAWELAQFIHHTSKKADVVLLCGDLNMHP----EDL 81
Cdd:cd09079  113 DYKSRKILGA-TIEINGQPIDVYSCHLGWWYD--------EEEPFAYEWSKLEKALAEAGRPVLLMGDFNNPAgsrgEGY 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  82 GCCLLKEWTGLHDAYLETRDfkgseeGNTmVPKNcyVSQQElkPFPFGVRIDYVLYKAvsgfYISCKSFETTtgFDPHRG 161
Cdd:cd09079  184 DLISSLGLQDTYDLAEEKDG------GVT-VEKA--IDGWR--GNKEAKRIDYIFVNR----KVKVKSSRVI--FNGKNP 246

                        170
                 ....*....|...
gi 767943466 162 TPLSDHEALMATL 174
Cdd:cd09079  247 PIVSDHFGVEVEL 259
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 6-76 6.99e-04

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 39.51  E-value: 6.99e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767943466   6 DWFSGKAVGLLVLHLSGMVLNAYVTHLHAEYNRqkdiylaHRVAQAWELAQFIHHTSKKADVVlLCGDLNM 76
Cdd:COG3568   66 PGGEPRGALWADVDVPGKPLRVVNTHLDLRSAA-------ARRRQARALAELLAELPAGAPVI-LAGDFND 128
 
Name Accession Description Interval E-value
RgfB-like cd09079
Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, ...
 6-174 2.07e-11

Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, and related proteins; This family includes Streptococcus agalactiae RgfB (for regulator of fibrinogen binding) and related proteins. The function of RgfB is unknown. It is part of a putative two component signal transduction system designated rgfBDAC (the rgf locus was identified in a screen for mutants of Streptococcus agalactiae with altered binding to fibrinogen). RgfA,-C,and -D do not belong to this superfamily: rgfA encodes a putative response regulator, and rgfC, a putative histidine kinase. All four genes are co-transcribed, and may be involved in regulating expression of bacterial cell surface components. 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: 197313 [Multi-domain]  Cd Length: 259  Bit Score: 63.05  E-value: 2.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466   6 DWFSGKAVGLlVLHLSGMVLNAYVTHLHAEYNrqkdiylaHRVAQAWELAQFIHHTSKKADVVLLCGDLNMHP----EDL 81
Cdd:cd09079  113 DYKSRKILGA-TIEINGQPIDVYSCHLGWWYD--------EEEPFAYEWSKLEKALAEAGRPVLLMGDFNNPAgsrgEGY 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  82 GCCLLKEWTGLHDAYLETRDfkgseeGNTmVPKNcyVSQQElkPFPFGVRIDYVLYKAvsgfYISCKSFETTtgFDPHRG 161
Cdd:cd09079  184 DLISSLGLQDTYDLAEEKDG------GVT-VEKA--IDGWR--GNKEAKRIDYIFVNR----KVKVKSSRVI--FNGKNP 246

                        170
                 ....*....|...
gi 767943466 162 TPLSDHEALMATL 174
Cdd:cd09079  247 PIVSDHFGVEVEL 259
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 30-174 8.40e-09

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. 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: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 55.43  E-value: 8.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  30 THL-----HAEYnrqkdiylahRVAQAWELAQFIHHTSKKADVVLlCGDLNMHPEDLGCCLLKEwtGLHDAYLETRDFKg 104
Cdd:cd09080  116 THLeslksHSSE----------RTAQLEEIAKKLKKPPGAANVIL-GGDFNLRDKEDDTGGLPN--GFVDAWEELGPPG- 181

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767943466 105 sEEGNTM-VPKNCYVSQQELKPFpfgVRIDYVLYKAvSGFyiSCKSFEtTTGFDP----HRGTPLSDHEALMATL 174
Cdd:cd09080  182 -EPGYTWdTQKNPMLRKGEAGPR---KRFDRVLLRG-SDL--KPKSIE-LIGTEPipgdEEGLFPSDHFGLLAEL 248
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 6-174 4.64e-08

Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine; Sphingomyelinases (SMase) are phosphodiesterases that catalyze the hydrolysis of sphingomyelin to ceramide and phosphorylcholine. Eukaryotic SMases have been classified according to their pH optima and are known as acid SMase, alkaline SMase, and neutral SMase (nSMase). Eukaryotic proteins in this family are nSMases, and are activated by a variety of stress-inducing agents such as cytokines or UV radiation. Ceramides and other metabolic derivatives, including sphingosine, are lipid "second messenger" molecules that participate in the regulation of stress-induced cellular responses, including cell death, adhesion, differentiation, and proliferation. Bacterial neutral SMases, which also belong to this domain family, are secreted proteins that act as membrane-damaging virulence factors. They promote colonization of the host tissue. 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: 197312 [Multi-domain]  Cd Length: 280  Bit Score: 53.50  E-value: 4.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466   6 DWFSGKAV--------GLLVLHLSGmvlnayvTHLHAEYNRQKDIylAHRVAQAWELAQFIH-HTSKKADVVLLCGDLN- 75
Cdd:cd09078  108 DCLAAKGVlyakinkgGTKVYHVFG-------THLQASDGSCLDR--AVRQKQLDELRAFIEeKNIPDNEPVIIAGDFNv 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  76 --MHPEDLgccllkewtgLHDAYLETRDFKGSE---EGNTMVPK--NCYVSQQELKPFPFGVRIDYVLYKAVSGFYISCK 148
Cdd:cd09078  179 dkRSSRDE----------YDDMLEQLHDYNAPEpitAGETPLTWdpGTNLLAKYNYPGGGGERLDYILYSNDHLQPSSWS 248

                        170       180       190
                 ....*....|....*....|....*....|..
gi 767943466 149 S----FETTTGFDPHRG--TPLSDHEALMATL 174
Cdd:cd09078  249 NevevPKSPTWSVTNGYtfADLSDHYPVSATF 280
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 14-174 4.36e-07

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: 50.17  E-value: 4.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  14 GLLVLHLSGMVLNAYV--THLHAEYNRQKDiylahRVAQAWELAQFI-HHTSKKADVVLLCGDLNMHPEDLGCCLLKEW- 89
Cdd:cd08372   97 RAVVVKFDVHDKELCVvnAHLQAGGTRADV-----RDAQLKEVLEFLkRLRQPNSAPVVICGDFNVRPSEVDSENPSSMl 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  90 TGLHdayleTRDFKGSEEGNTMVPKNcyvsqqELKPFPFGVRIDYVLYKAvsGFYISCKSFETTTgfDPHRGTPLSDHEA 169
Cdd:cd08372  172 RLFV-----ALNLVDSFETLPHAYTF------DTYMHNVKSRLDYIFVSK--SLLPSVKSSKILS--DAARARIPSDHYP 236


                 ....*
gi 767943466 170 LMATL 174
Cdd:cd08372  237 IEVTL 241
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 13-174 6.04e-06

Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; 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: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 46.83  E-value: 6.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  13 VGLLVLHLSGMVLNAYVTHL--HAEYNRQKDIYLahrvaqaweLAQFIHHTSKKADVVLlCGDLNMHPEDLGCCLLKEwT 90
Cdd:cd09083  116 WARFKDKKTGKEFYVFNTHLdhVGEEAREESAKL---------ILERIKEIAGDLPVIL-TGDFNAEPDSEPYKTLTS-G 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  91 GLHDAYLETRDFKGSEEGnTMvpkncyvsqQELKPFPFGVRIDYVLYKavSGFYisCKSFET-TTGFDphrGTPLSDHEA 169
Cdd:cd09083  185 GLKDARDTAATTDGGPEG-TF---------HGFKGPPGGSRIDYIFVS--PGVK--VLSYEIlTDRYD---GRYPSDHFP 247


                 ....*
gi 767943466 170 LMATL 174
Cdd:cd09083  248 VVADL 252
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 47-174 3.75e-05

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: 44.21  E-value: 3.75e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943466  47 RVAQAWELAQFIHHTSKKadvVLLCGDLNMHPEDLGCCLLKEwtGLHDAYLEtrdfKGSEEGNTmvpkncyvsqqeLKPF 126
Cdd:cd09084  151 RAAQADLLAADIAASPYP---VIVCGDFNDTPASYVYRTLKK--GLTDAFVE----AGSGFGYT------------FNGL 209

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 767943466 127 PFGVRIDYVLYKAvsgfYISCKSFETTTGfdphrgtPLSDHEALMATL 174
Cdd:cd09084  210 FFPLRIDYILTSK----GFKVLRYRVDPG-------KYSDHYPIVATL 246
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 6-76 6.99e-04

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 39.51  E-value: 6.99e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767943466   6 DWFSGKAVGLLVLHLSGMVLNAYVTHLHAEYNRqkdiylaHRVAQAWELAQFIHHTSKKADVVlLCGDLNM 76
Cdd:COG3568   66 PGGEPRGALWADVDVPGKPLRVVNTHLDLRSAA-------ARRRQARALAELLAELPAGAPVI-LAGDFND 128
 
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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