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Conserved domains on  [gi|1015172283|ref|NP_001308934|]
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mismatch repair endonuclease PMS2 isoform b [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
mutl super family cl36694
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
5-209 1.75e-67

DNA mismatch repair protein MutL; All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00585:

Pssm-ID: 273155 [Multi-domain]  Cd Length: 312  Bit Score: 224.83  E-value: 1.75e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283   5 NGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKeFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNqlgQGKRQPVVCTGG 84
Cdd:TIGR00585 128 GGMIESIKPAPRPVGTTVEVRDLFYNLPVRRK-FLKSPKKEFRKILDVLQRYALIHPDISFSLTH---DGKKVLQLSTKP 203
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  85 SPSIKEN-IGSVFGQKQLQSLIPFVQLPPSDsvceeyglscsdalhnlFYISGFISQCTHGVGRSSTDrQFFFINRRPCD 163
Cdd:TIGR00585 204 NQSTKENrIRSVFGTAVLRKLIPLDEWEDLD-----------------LQLEGFISQPNVTRSRRSGW-QFLFINGRPVE 265
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1015172283 164 PAKVCRLVNEVYHMYN-RHQYPFVVLNISVDSECVDINVTPDKRQIL 209
Cdd:TIGR00585 266 LKLLLKAIREVYHEYLpKGQYPVFVLNLEIDPELVDVNVHPDKKEVR 312
MutL super family cl33837
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
2-721 5.59e-60

DNA mismatch repair ATPase MutL [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0323:

Pssm-ID: 223400 [Multi-domain]  Cd Length: 638  Bit Score: 213.74  E-value: 5.59e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283   2 FDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKeFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQlgqGK-RQPVV 80
Cdd:COG0323   126 AEGGGMEVTVKPAAHPVGTTVEVRDLFYNTPARRK-FLKSEKTEFGHITELINRYALAHPDISFSLSHN---GKlRIELL 201
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  81 CTGGSPSIKENIGSVFGQKQLQSLIPFvqlppsdsvceeyglscsDALHNLFYISGFISQCThgVGRSSTDRQFFFINRR 160
Cdd:COG0323   202 KLPGTGDLEERIAAVYGTEFLKNALPI------------------ENEHEDLRLSGYVSLPE--FTRASRDYQYLFVNGR 261
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 161 PCDPAKVCRLVNEVYHMYN-RHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLigmfdsdvnKLNVSQ 239
Cdd:COG0323   262 PVRDKLLNHALREAYADYLpRGRYPVFVLFLELDPELVDVNVHPAKKEVRFSDERLVHDLIYEAI---------KEALAQ 332
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 240 QPLLdvegnlikmHAADLEKPMVEKQdQSPSLRTGEEKKDVSISRLREAFSLRHTTENKPHSPKTPEPRRSPLGQKRGML 319
Cdd:COG0323   333 QGLI---------PPASVEAPKSASQ-PLPAFQEPSPLPESRIQKSKVAKSGSSKSDAPSIAEPASGASPSPASPSIRPL 402
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 320 SSSTSgAISDKGVLRPQKEAVSSSHGPSDPTDraevekdsghgstsvdsegfsipdtgshcsseyaasspgdrgsqehvd 399
Cdd:COG0323   403 SKNIL-PESSPGSLKNEDRSYDDLLEEPAESE------------------------------------------------ 433
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 400 sqekapktddsfsdvdchsnqedtgckfrvlpqptnlatpntkrfkkeeilsssdicqklvntqdmsasqvdvavkinkk 479
Cdd:COG0323       --------------------------------------------------------------------------------
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 480 vvpldfsmsslakrikqlhheaqqsegeqnyrkfrakicpgenQAAEDELRKEISKTMFAEMEIIGQFNLGFIITKLNED 559
Cdd:COG0323   434 -------------------------------------------DKQEEAEQKAISEDVFPLGEAIGQVHGTYILAEHEDG 470
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 560 IFIVDQHATDEKYNFEMLQQ--HTVLQGQRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDFVIDENapvtERAKLISLPT 637
Cdd:COG0323   471 LVLVDQHAAHERILYEKLKNelGNVGELQPLLIPIRLELSPEEADVLEEHKEELEKLGFEIESFGE----NSVAVRSVPA 546
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 638 SKNWTFGPQDVDELIFMLSdSPGVMCRPSRVKQMFASRACRKSVMIGTALNTSEMKKLITHMGEMDHPWNCPHGRPTMRH 717
Cdd:COG0323   547 MLGKAEVQELIRELLDDLL-EGKLKDLKELLEELAATMACRSAVKAGRELSAEEMNALLRDLEACPNPWTCPHGRPTYIV 625

                  ....
gi 1015172283 718 IANL 721
Cdd:COG0323   626 LSLA 629
 
Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
5-209 1.75e-67

DNA mismatch repair protein MutL; All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. 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: 273155 [Multi-domain]  Cd Length: 312  Bit Score: 224.83  E-value: 1.75e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283   5 NGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKeFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNqlgQGKRQPVVCTGG 84
Cdd:TIGR00585 128 GGMIESIKPAPRPVGTTVEVRDLFYNLPVRRK-FLKSPKKEFRKILDVLQRYALIHPDISFSLTH---DGKKVLQLSTKP 203
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  85 SPSIKEN-IGSVFGQKQLQSLIPFVQLPPSDsvceeyglscsdalhnlFYISGFISQCTHGVGRSSTDrQFFFINRRPCD 163
Cdd:TIGR00585 204 NQSTKENrIRSVFGTAVLRKLIPLDEWEDLD-----------------LQLEGFISQPNVTRSRRSGW-QFLFINGRPVE 265
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1015172283 164 PAKVCRLVNEVYHMYN-RHQYPFVVLNISVDSECVDINVTPDKRQIL 209
Cdd:TIGR00585 266 LKLLLKAIREVYHEYLpKGQYPVFVLNLEIDPELVDVNVHPDKKEVR 312
MutL_Trans_hPMS_2_like cd03484
MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
87-229 2.66e-67

MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2). hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome.


Pssm-ID: 239566 [Multi-domain]  Cd Length: 142  Bit Score: 217.91  E-value: 2.66e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  87 SIKENIGSVFGQKQLQSLIPFVQLPPSDSVCEEYgLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAK 166
Cdd:cd03484     1 DIKDNIINVFGGKVIKGLIPINLELDVNPTKEEL-DSDEDLADSEVKITGYISKPSHGCGRSSSDRQFFYINGRPVDLKK 79
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1015172283 167 VCRLVNEVYHMYNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLIGMFD 229
Cdd:cd03484    80 VAKLINEVYKSFNSRQYPFFILNISLPTSLYDVNVTPDKRTVLLHDEDRLIDTLKTSLSELFE 142
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
2-721 5.59e-60

DNA mismatch repair ATPase MutL [Replication, recombination and repair];


Pssm-ID: 223400 [Multi-domain]  Cd Length: 638  Bit Score: 213.74  E-value: 5.59e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283   2 FDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKeFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQlgqGK-RQPVV 80
Cdd:COG0323   126 AEGGGMEVTVKPAAHPVGTTVEVRDLFYNTPARRK-FLKSEKTEFGHITELINRYALAHPDISFSLSHN---GKlRIELL 201
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  81 CTGGSPSIKENIGSVFGQKQLQSLIPFvqlppsdsvceeyglscsDALHNLFYISGFISQCThgVGRSSTDRQFFFINRR 160
Cdd:COG0323   202 KLPGTGDLEERIAAVYGTEFLKNALPI------------------ENEHEDLRLSGYVSLPE--FTRASRDYQYLFVNGR 261
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 161 PCDPAKVCRLVNEVYHMYN-RHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLigmfdsdvnKLNVSQ 239
Cdd:COG0323   262 PVRDKLLNHALREAYADYLpRGRYPVFVLFLELDPELVDVNVHPAKKEVRFSDERLVHDLIYEAI---------KEALAQ 332
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 240 QPLLdvegnlikmHAADLEKPMVEKQdQSPSLRTGEEKKDVSISRLREAFSLRHTTENKPHSPKTPEPRRSPLGQKRGML 319
Cdd:COG0323   333 QGLI---------PPASVEAPKSASQ-PLPAFQEPSPLPESRIQKSKVAKSGSSKSDAPSIAEPASGASPSPASPSIRPL 402
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 320 SSSTSgAISDKGVLRPQKEAVSSSHGPSDPTDraevekdsghgstsvdsegfsipdtgshcsseyaasspgdrgsqehvd 399
Cdd:COG0323   403 SKNIL-PESSPGSLKNEDRSYDDLLEEPAESE------------------------------------------------ 433
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 400 sqekapktddsfsdvdchsnqedtgckfrvlpqptnlatpntkrfkkeeilsssdicqklvntqdmsasqvdvavkinkk 479
Cdd:COG0323       --------------------------------------------------------------------------------
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 480 vvpldfsmsslakrikqlhheaqqsegeqnyrkfrakicpgenQAAEDELRKEISKTMFAEMEIIGQFNLGFIITKLNED 559
Cdd:COG0323   434 -------------------------------------------DKQEEAEQKAISEDVFPLGEAIGQVHGTYILAEHEDG 470
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 560 IFIVDQHATDEKYNFEMLQQ--HTVLQGQRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDFVIDENapvtERAKLISLPT 637
Cdd:COG0323   471 LVLVDQHAAHERILYEKLKNelGNVGELQPLLIPIRLELSPEEADVLEEHKEELEKLGFEIESFGE----NSVAVRSVPA 546
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 638 SKNWTFGPQDVDELIFMLSdSPGVMCRPSRVKQMFASRACRKSVMIGTALNTSEMKKLITHMGEMDHPWNCPHGRPTMRH 717
Cdd:COG0323   547 MLGKAEVQELIRELLDDLL-EGKLKDLKELLEELAATMACRSAVKAGRELSAEEMNALLRDLEACPNPWTCPHGRPTYIV 625

                  ....
gi 1015172283 718 IANL 721
Cdd:COG0323   626 LSLA 629
MutL_C smart00853
MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair ...
543-686 8.74e-38

MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.


Pssm-ID: 214857 [Multi-domain]  Cd Length: 140  Bit Score: 137.49  E-value: 8.74e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  543 IIGQFNLGFIITKLNEDIFIVDQHATDEKYNFEMLQQHTV-LQGQRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDFVID 621
Cdd:smart00853   1 ALGQVAGTYILAEREDGLYLLDQHAAHERILYEQLLKQAGgLESQPLLIPVRLELSPQEAALLEEHLELLRQLGFELEIF 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1015172283  622 ENAPVTerakLISLPTSKNWTFGPQDVDELIFMLSDSPGVMCrPSRVKQMFASRACRKSVMIGTA 686
Cdd:smart00853  81 GPQSLI----LRSVPALLRQQNLQKLIPELLDLLSDEEENAR-PSRLEALLASLACRSAIRAGDA 140
MutL_C pfam08676
MutL C terminal dimerization domain; MutL and MutS are key components of the DNA repair ...
544-687 2.37e-29

MutL C terminal dimerization domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognizes mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerization.


Pssm-ID: 430147  Cd Length: 145  Bit Score: 113.47  E-value: 2.37e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 544 IGQFNLGFIITKLNEDIFIVDQHATDEKYNFEMLQQHTVLQG---QRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDFvi 620
Cdd:pfam08676   4 LGQVHGTYILAENEDGLYLIDQHAAHERILYEKLKRALAEGGlaaQPLLIPLVLELSPEEAALLEEHKEELAQLGFEL-- 81
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1015172283 621 deNAPVTERAKLISLPTSKNWTFGPQDVDELIFMLSDSPGVMCrPSRVKQMFASRACRKSVMIGTAL 687
Cdd:pfam08676  82 --EEFGPNSVIVRSVPALLRQQNLQELIRELLDELAEKGGSSL-EESLEELLATMACHSAVRAGRRL 145
mutL PRK00095
DNA mismatch repair endonuclease MutL;
4-718 1.23e-25

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 112.23  E-value: 1.23e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283   4 HNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKeFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNqlgQGKrqPVVCTG 83
Cdd:PRK00095  126 EGGEIVEVKPAAHPVGTTIEVRDLFFNTPARRK-FLKSEKTELGHIDDVVNRLALAHPDVAFTLTH---NGK--LVLQTR 199
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  84 GSPSIKENIGSVFGQKQLQSLIPFvqlppsdsvceeyglscsDALHNLFYISGFISQ--CThgvgRSSTDRQFFFINRRP 161
Cdd:PRK00095  200 GAGQLLQRLAAILGREFAENALPI------------------DAEHGDLRLSGYVGLptLS----RANRDYQYLFVNGRY 257
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 162 cdpakV-CRLVN----EVYHMY-NRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLlavlktsligmfdsdvnkl 235
Cdd:PRK00095  258 -----VrDKLLNhairQAYHDLlPRGRYPAFVLFLELDPHQVDVNVHPAKHEVRFRDERLV------------------- 313
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 236 nvsqqplldveGNLIkmhaadlekpmvekqdqspslrtgeekkdvsISRLREAFslrhttenkphspktpeprrsplgqK 315
Cdd:PRK00095  314 -----------HDLI-------------------------------VQAIQEAL-------------------------A 326
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 316 RGMLSSSTSGAISDKGVLRPQKEAVSSSHGPSDPTdraevekdsghgstsvdsegfsipdtgshcsseyAASSPGDRGSQ 395
Cdd:PRK00095  327 QSGLIPAAAGANQVLEPAEPEPLPLQQTPLYASGS----------------------------------SPPASSPSSAP 372
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 396 EHVDSQEKAPKTDDSFSDVDCHSNQEDTGCKFRVLPQPTNLATPntkrfkkeeilsssdicqklvntqdmsasqvdvavk 475
Cdd:PRK00095  373 PEQSEESQEESSAEKNPLQPNASQSEAAAAASAEAAAAAPAAAP------------------------------------ 416
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 476 inkkvvpldfsmsslakrikqlhhEAQQSEGEQNYrkfrakicpgenqaaedelrkeisktmFAEMEIIGQFNLGFIITK 555
Cdd:PRK00095  417 ------------------------EPAEAAEEADS---------------------------FPLGYALGQLHGTYILAE 445
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 556 LNEDIFIVDQHATDEKYNFEMLQQH---TVLQGQRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDF-VIDENApVTERak 631
Cdd:PRK00095  446 NEDGLYLVDQHAAHERLLYEQLKDKlaeVGLASQPLLIPLVLELSEDEADRLEEHKELLARLGLELePFGPNS-FAVR-- 522
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 632 liSLPTsknWtFGPQDVDELIF----MLSDSPGVmcRPSRVKQMFASRACRKSVMIGTALNTSEMKKLITHMGEMDHPWN 707
Cdd:PRK00095  523 --EVPA---L-LGQQELEELIRdlldELAEEGDS--DTLKERELLATMACHGAIRAGRRLTLEEMNALLRQLEATENPGT 594
                         730
                  ....*....|.
gi 1015172283 708 CPHGRPTMRHI 718
Cdd:PRK00095  595 CPHGRPTYIEL 605
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
94-224 9.29e-24

DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold.


Pssm-ID: 426060 [Multi-domain]  Cd Length: 117  Bit Score: 96.80  E-value: 9.29e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  94 SVFGQKQLQSLIPFvqlppsdsvceeyglscsDALHNLFYISGFISQctHGVGRSSTDRQFFFINRRPCDPAKVCRLVNE 173
Cdd:pfam01119   2 AIYGKEFAENLLPI------------------EKEDDGLRLSGYISK--PTLSRSNRDYQYLFVNGRPVRDKLLSHAIRE 61
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1015172283 174 VYHMY-NRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSL 224
Cdd:pfam01119  62 AYRDLlPKGRYPVAVLFLEIDPELVDVNVHPTKREVRFRDEREVYDFIKEAL 113
 
Name Accession Description Interval E-value
mutl TIGR00585
DNA mismatch repair protein MutL; All proteins in this family for which the functions are ...
5-209 1.75e-67

DNA mismatch repair protein MutL; All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. 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: 273155 [Multi-domain]  Cd Length: 312  Bit Score: 224.83  E-value: 1.75e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283   5 NGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKeFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNqlgQGKRQPVVCTGG 84
Cdd:TIGR00585 128 GGMIESIKPAPRPVGTTVEVRDLFYNLPVRRK-FLKSPKKEFRKILDVLQRYALIHPDISFSLTH---DGKKVLQLSTKP 203
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  85 SPSIKEN-IGSVFGQKQLQSLIPFVQLPPSDsvceeyglscsdalhnlFYISGFISQCTHGVGRSSTDrQFFFINRRPCD 163
Cdd:TIGR00585 204 NQSTKENrIRSVFGTAVLRKLIPLDEWEDLD-----------------LQLEGFISQPNVTRSRRSGW-QFLFINGRPVE 265
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1015172283 164 PAKVCRLVNEVYHMYN-RHQYPFVVLNISVDSECVDINVTPDKRQIL 209
Cdd:TIGR00585 266 LKLLLKAIREVYHEYLpKGQYPVFVLNLEIDPELVDVNVHPDKKEVR 312
MutL_Trans_hPMS_2_like cd03484
MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
87-229 2.66e-67

MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2). hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome.


Pssm-ID: 239566 [Multi-domain]  Cd Length: 142  Bit Score: 217.91  E-value: 2.66e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  87 SIKENIGSVFGQKQLQSLIPFVQLPPSDSVCEEYgLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAK 166
Cdd:cd03484     1 DIKDNIINVFGGKVIKGLIPINLELDVNPTKEEL-DSDEDLADSEVKITGYISKPSHGCGRSSSDRQFFYINGRPVDLKK 79
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1015172283 167 VCRLVNEVYHMYNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLIGMFD 229
Cdd:cd03484    80 VAKLINEVYKSFNSRQYPFFILNISLPTSLYDVNVTPDKRTVLLHDEDRLIDTLKTSLSELFE 142
MutL COG0323
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
2-721 5.59e-60

DNA mismatch repair ATPase MutL [Replication, recombination and repair];


Pssm-ID: 223400 [Multi-domain]  Cd Length: 638  Bit Score: 213.74  E-value: 5.59e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283   2 FDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKeFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQlgqGK-RQPVV 80
Cdd:COG0323   126 AEGGGMEVTVKPAAHPVGTTVEVRDLFYNTPARRK-FLKSEKTEFGHITELINRYALAHPDISFSLSHN---GKlRIELL 201
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  81 CTGGSPSIKENIGSVFGQKQLQSLIPFvqlppsdsvceeyglscsDALHNLFYISGFISQCThgVGRSSTDRQFFFINRR 160
Cdd:COG0323   202 KLPGTGDLEERIAAVYGTEFLKNALPI------------------ENEHEDLRLSGYVSLPE--FTRASRDYQYLFVNGR 261
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 161 PCDPAKVCRLVNEVYHMYN-RHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLigmfdsdvnKLNVSQ 239
Cdd:COG0323   262 PVRDKLLNHALREAYADYLpRGRYPVFVLFLELDPELVDVNVHPAKKEVRFSDERLVHDLIYEAI---------KEALAQ 332
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 240 QPLLdvegnlikmHAADLEKPMVEKQdQSPSLRTGEEKKDVSISRLREAFSLRHTTENKPHSPKTPEPRRSPLGQKRGML 319
Cdd:COG0323   333 QGLI---------PPASVEAPKSASQ-PLPAFQEPSPLPESRIQKSKVAKSGSSKSDAPSIAEPASGASPSPASPSIRPL 402
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 320 SSSTSgAISDKGVLRPQKEAVSSSHGPSDPTDraevekdsghgstsvdsegfsipdtgshcsseyaasspgdrgsqehvd 399
Cdd:COG0323   403 SKNIL-PESSPGSLKNEDRSYDDLLEEPAESE------------------------------------------------ 433
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 400 sqekapktddsfsdvdchsnqedtgckfrvlpqptnlatpntkrfkkeeilsssdicqklvntqdmsasqvdvavkinkk 479
Cdd:COG0323       --------------------------------------------------------------------------------
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 480 vvpldfsmsslakrikqlhheaqqsegeqnyrkfrakicpgenQAAEDELRKEISKTMFAEMEIIGQFNLGFIITKLNED 559
Cdd:COG0323   434 -------------------------------------------DKQEEAEQKAISEDVFPLGEAIGQVHGTYILAEHEDG 470
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 560 IFIVDQHATDEKYNFEMLQQ--HTVLQGQRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDFVIDENapvtERAKLISLPT 637
Cdd:COG0323   471 LVLVDQHAAHERILYEKLKNelGNVGELQPLLIPIRLELSPEEADVLEEHKEELEKLGFEIESFGE----NSVAVRSVPA 546
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 638 SKNWTFGPQDVDELIFMLSdSPGVMCRPSRVKQMFASRACRKSVMIGTALNTSEMKKLITHMGEMDHPWNCPHGRPTMRH 717
Cdd:COG0323   547 MLGKAEVQELIRELLDDLL-EGKLKDLKELLEELAATMACRSAVKAGRELSAEEMNALLRDLEACPNPWTCPHGRPTYIV 625

                  ....
gi 1015172283 718 IANL 721
Cdd:COG0323   626 LSLA 629
MutL_C smart00853
MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair ...
543-686 8.74e-38

MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.


Pssm-ID: 214857 [Multi-domain]  Cd Length: 140  Bit Score: 137.49  E-value: 8.74e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  543 IIGQFNLGFIITKLNEDIFIVDQHATDEKYNFEMLQQHTV-LQGQRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDFVID 621
Cdd:smart00853   1 ALGQVAGTYILAEREDGLYLLDQHAAHERILYEQLLKQAGgLESQPLLIPVRLELSPQEAALLEEHLELLRQLGFELEIF 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1015172283  622 ENAPVTerakLISLPTSKNWTFGPQDVDELIFMLSDSPGVMCrPSRVKQMFASRACRKSVMIGTA 686
Cdd:smart00853  81 GPQSLI----LRSVPALLRQQNLQKLIPELLDLLSDEEENAR-PSRLEALLASLACRSAIRAGDA 140
MutL_Trans cd00782
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
88-224 7.61e-37

MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome. Mutation in hMLH1 accounts for a large fraction of HNPCC families. There is no convincing evidence to support hPMS1 having a role in HNPCC predisposition. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH.


Pssm-ID: 238405 [Multi-domain]  Cd Length: 122  Bit Score: 134.21  E-value: 7.61e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  88 IKENIGSVFGQKQLQSLIPFvqlppsdsvceeyglscsDALHNLFYISGFISQCTHGvgRSSTDRQFFFINRRPCDPAKV 167
Cdd:cd00782     1 LKDRIAQVYGKEVAKNLIEV------------------ELESGDFRISGYISKPDFG--RSSKDRQFLFVNGRPVRDKLL 60
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1015172283 168 CRLVNEVYHMYN-RHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSL 224
Cdd:cd00782    61 SKAINEAYRSYLpKGRYPVFVLNLELPPELVDVNVHPTKREVRFSDEEEVLELIREAL 118
MutL_C pfam08676
MutL C terminal dimerization domain; MutL and MutS are key components of the DNA repair ...
544-687 2.37e-29

MutL C terminal dimerization domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognizes mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerization.


Pssm-ID: 430147  Cd Length: 145  Bit Score: 113.47  E-value: 2.37e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 544 IGQFNLGFIITKLNEDIFIVDQHATDEKYNFEMLQQHTVLQG---QRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDFvi 620
Cdd:pfam08676   4 LGQVHGTYILAENEDGLYLIDQHAAHERILYEKLKRALAEGGlaaQPLLIPLVLELSPEEAALLEEHKEELAQLGFEL-- 81
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1015172283 621 deNAPVTERAKLISLPTSKNWTFGPQDVDELIFMLSDSPGVMCrPSRVKQMFASRACRKSVMIGTAL 687
Cdd:pfam08676  82 --EEFGPNSVIVRSVPALLRQQNLQELIRELLDELAEKGGSSL-EESLEELLATMACHSAVRAGRRL 145
mutL PRK00095
DNA mismatch repair endonuclease MutL;
4-718 1.23e-25

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 112.23  E-value: 1.23e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283   4 HNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKeFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNqlgQGKrqPVVCTG 83
Cdd:PRK00095  126 EGGEIVEVKPAAHPVGTTIEVRDLFFNTPARRK-FLKSEKTELGHIDDVVNRLALAHPDVAFTLTH---NGK--LVLQTR 199
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  84 GSPSIKENIGSVFGQKQLQSLIPFvqlppsdsvceeyglscsDALHNLFYISGFISQ--CThgvgRSSTDRQFFFINRRP 161
Cdd:PRK00095  200 GAGQLLQRLAAILGREFAENALPI------------------DAEHGDLRLSGYVGLptLS----RANRDYQYLFVNGRY 257
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 162 cdpakV-CRLVN----EVYHMY-NRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLlavlktsligmfdsdvnkl 235
Cdd:PRK00095  258 -----VrDKLLNhairQAYHDLlPRGRYPAFVLFLELDPHQVDVNVHPAKHEVRFRDERLV------------------- 313
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 236 nvsqqplldveGNLIkmhaadlekpmvekqdqspslrtgeekkdvsISRLREAFslrhttenkphspktpeprrsplgqK 315
Cdd:PRK00095  314 -----------HDLI-------------------------------VQAIQEAL-------------------------A 326
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 316 RGMLSSSTSGAISDKGVLRPQKEAVSSSHGPSDPTdraevekdsghgstsvdsegfsipdtgshcsseyAASSPGDRGSQ 395
Cdd:PRK00095  327 QSGLIPAAAGANQVLEPAEPEPLPLQQTPLYASGS----------------------------------SPPASSPSSAP 372
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 396 EHVDSQEKAPKTDDSFSDVDCHSNQEDTGCKFRVLPQPTNLATPntkrfkkeeilsssdicqklvntqdmsasqvdvavk 475
Cdd:PRK00095  373 PEQSEESQEESSAEKNPLQPNASQSEAAAAASAEAAAAAPAAAP------------------------------------ 416
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 476 inkkvvpldfsmsslakrikqlhhEAQQSEGEQNYrkfrakicpgenqaaedelrkeisktmFAEMEIIGQFNLGFIITK 555
Cdd:PRK00095  417 ------------------------EPAEAAEEADS---------------------------FPLGYALGQLHGTYILAE 445
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 556 LNEDIFIVDQHATDEKYNFEMLQQH---TVLQGQRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDF-VIDENApVTERak 631
Cdd:PRK00095  446 NEDGLYLVDQHAAHERLLYEQLKDKlaeVGLASQPLLIPLVLELSEDEADRLEEHKELLARLGLELePFGPNS-FAVR-- 522
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 632 liSLPTsknWtFGPQDVDELIF----MLSDSPGVmcRPSRVKQMFASRACRKSVMIGTALNTSEMKKLITHMGEMDHPWN 707
Cdd:PRK00095  523 --EVPA---L-LGQQELEELIRdlldELAEEGDS--DTLKERELLATMACHGAIRAGRRLTLEEMNALLRQLEATENPGT 594
                         730
                  ....*....|.
gi 1015172283 708 CPHGRPTMRHI 718
Cdd:PRK00095  595 CPHGRPTYIEL 605
DNA_mis_repair pfam01119
DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain ...
94-224 9.29e-24

DNA mismatch repair protein, C-terminal domain; This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold.


Pssm-ID: 426060 [Multi-domain]  Cd Length: 117  Bit Score: 96.80  E-value: 9.29e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  94 SVFGQKQLQSLIPFvqlppsdsvceeyglscsDALHNLFYISGFISQctHGVGRSSTDRQFFFINRRPCDPAKVCRLVNE 173
Cdd:pfam01119   2 AIYGKEFAENLLPI------------------EKEDDGLRLSGYISK--PTLSRSNRDYQYLFVNGRPVRDKLLSHAIRE 61
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1015172283 174 VYHMY-NRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSL 224
Cdd:pfam01119  62 AYRDLlPKGRYPVAVLFLEIDPELVDVNVHPTKREVRFRDEREVYDFIKEAL 113
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
1-70 1.58e-19

Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains; This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease.


Pssm-ID: 340403 [Multi-domain]  Cd Length: 188  Bit Score: 86.72  E-value: 1.58e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283   1 MFDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKeFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQ 70
Cdd:cd16926   115 VVDGGGIIEEVKPAAAPVGTTVTVRDLFYNTPARRK-FLKSPKTELSKILDLVQRLALAHPDVSFSLTHD 183
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
88-209 2.29e-19

MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.


Pssm-ID: 238202 [Multi-domain]  Cd Length: 107  Bit Score: 83.85  E-value: 2.29e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  88 IKENIGSVFGQKQLQSLIPFvqlppsdsvceeyglscsDALHNLFYISGFISQCTHGvgRSSTDRQFFFINRRPCDPAK- 166
Cdd:cd00329     1 LKDRLAEILGDKVADKLIYV------------------EGESDGFRVEGAISYPDSG--RSSKDRQFSFVNGRPVREGGt 60
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1015172283 167 VCRLVNEVYHMY----NRHQYPFVVLNISVDSECVDINVTPDKRQIL 209
Cdd:cd00329    61 HVKAVREAYTRAlngdDVRRYPVAVLSLKIPPSLVDVNVHPTKEEVR 107
MutL_Trans_hPMS_1_like cd03485
MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
87-219 1.79e-11

MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition.


Pssm-ID: 239567 [Multi-domain]  Cd Length: 132  Bit Score: 61.90  E-value: 1.79e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  87 SIKENIGSVFGQKQLQSLIPFvqlppsDSVCEEYGlscsdalhnlFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAK 166
Cdd:cd03485     1 DHKEALARVLGTAVAANMVPV------QSTDEDPQ----------ISLEGFLPKPGSDVSKTKSDGKFISVNSRPVSLGK 64
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1015172283 167 -VCRLVNEVYHMYNRH----QYPFVVLNISVDSECVDINVTPDKRQILLQ-EEKLLLAV 219
Cdd:cd03485    65 dIGKLLRQYYSSAYRKsslrRYPVFFLNILCPPGLVDVNIEPDKDDVLLQnKEAVLQAV 123
MutL_Trans_MLH1 cd03483
MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
87-213 9.46e-10

MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.


Pssm-ID: 239565 [Multi-domain]  Cd Length: 127  Bit Score: 56.86  E-value: 9.46e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283  87 SIKENIGSVFGQKQLQSLIPFvqlppSDSVCEEYGLscsdalhnlFYISGFISQCTHgvgrSSTDRQF-FFINRR--PCD 163
Cdd:cd03483     1 STKDNIRSVYGAAVANELIEV-----EISDDDDDLG---------FKVKGLISNANY----SKKKIIFiLFINNRlvECS 62
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1015172283 164 PAKvcRLVNEVYHMY-NRHQYPFVVLNISVDSECVDINVTPDKRQI--LLQEE 213
Cdd:cd03483    63 ALR--RAIENVYANYlPKGAHPFVYLSLEIPPENVDVNVHPTKREVhfLNEEE 113
MutL_Trans_MutL cd03482
MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
124-208 6.67e-05

MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.


Pssm-ID: 239564 [Multi-domain]  Cd Length: 123  Bit Score: 42.96  E-value: 6.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 124 CSDALHNLFY-----ISGFISQCTHGvgRSSTDRQFFFINRRPC-DpakvcRLVN----EVYHMYNRHQ-YPFVVLNISV 192
Cdd:cd03482    14 AEQALAIDEEagglrLSGWIALPTFA--RSQADIQYFYVNGRMVrD-----KLIShavrQAYSDVLHGGrHPAYVLYLEL 86
                          90
                  ....*....|....*.
gi 1015172283 193 DSECVDINVTPDKRQI 208
Cdd:cd03482    87 DPAQVDVNVHPAKHEV 102
MutL_Trans_MLH3 cd03486
MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in ...
120-220 4.71e-04

MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH3 (MutL homologue 3). MLH3 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with MLH3. The MLH1-MLH3 complex plays a role in meiosis. A role for hMLH1-hMLH3 in DNA mismatch repair (MMR) has not been established. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC.


Pssm-ID: 239568 [Multi-domain]  Cd Length: 141  Bit Score: 40.76  E-value: 4.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015172283 120 YGLSCSDAL------HNLFYISGFISQCTHGvgrsSTDRQFFFINRRPCDPAKVCRLVNEVY------------------ 175
Cdd:cd03486    10 YGLVLAQKLkevsakFQEYEVSGYISSEGHY----SKSFQFIYVNGRLYLKTRFHKLINKLFrktsavaknksspqskss 85
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1015172283 176 --HMYNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVL 220
Cdd:cd03486    86 rrGKRSQESYPVFVLNITCPASEYDLSQEPSKTIIEFKDWKTLLPLI 132
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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