1JX4,1N48,1K1Q,2OH2


Conserved Protein Domain Family
PolY_Pol_IV_kappa

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cd03586: PolY_Pol_IV_kappa 
Click on image for an interactive view with Cn3D
DNA Polymerase IV/Kappa
Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a higher error rate than other Y-family polymerases.
Statistics
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PSSM-Id: 176459
View PSSM: cd03586
Aligned: 130 rows
Threshold Bit Score: 233.567
Threshold Setting Gi: 23208515
Created: 3-Apr-2006
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active siteDNA binding
Conserved site includes 11 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        ## ###                               ##  #  #                                
1JX4_A      4 LFVDFDYFYAQVEEVLnpslkGKPVVVCVfsgrfedsgaVATANYEARKFGvk-agIPIVEAKKILPnavylpxrkevYQ 82  Sulfolobus solfata...
AAS91582  106 LHVDMDAFYAAVETLSdpsikGKPMAVGGls-------mISTANYEARKFGvr-aaMPGFIARKLCPdlifvpvdftkYT 177 thale cress
AAW46481  222 IHVDMDAFYASVEVQRdpslkGKAFGVGKg--------vLCTASYEARKFGvr-saMAGFIAKKLCPhiiltdlhfdlYT 292 Cryptococcus neofo...
EAK83015  149 LHTDIDMFYAAVELARdpslkGKCFGVGSg--------vLVTASYEARRGYgvrsgMAVFVAKALCPhlivvkndmqsYV 220 Ustilago maydis 521
EAN79815  136 IHLDMDMFYAAVEIKKhpeyaAIPLAVGSvs-------mLSTANYVARECGir-sgMPGYIGLKVCPnllilppdfdaYN 207 Trypanosoma brucei
EAN87784  118 VHVDMDMFYAAVEMKKnpslvDVPLGVGTfd-------mLSTTNYVARRYGvr-sgMPGYIGVKLCPslvivptdfdaYH 189 Trypanosoma cruzi
CAJ05435  146 IHIDMDMFYAAVEEKKtpslrGKPFGVGSqq-------mLSTTNYIARQYGvr-sgMPGFIGKKLCPeliivpndfpaYQ 217 Leishmania major
CAJ05431  234 VHMDMDMFFAAVEMKKnpqyaEVPLGIGSms-------mLSTTNYVARKYGvq-sgMPGFIGMRLCPqlvivptdfaaCR 305 Leishmania major
AAN15780  104 VHIDMDAFYAAVEMRDnpelkDKPIAVGSms-------mLSTSNYHARRFGvr-aaMPGFIAKRLCPqliivppnfdkYR 175 human
O74944    133 VHVDCDAFYASIEELKnpklkSLPMAVGKs--------vLCTANYVARKFGvr-saMPEFIARKICPdlvviplnlseYA 203 fission yeast
Feature 1                           #                                                         
1JX4_A     83 QVSSRIXNLLreysekieIASIDEAYLDIsdk------------------------------------------------ 114 Sulfolobus solfata...
AAS91582  178 HYSDLTRKVFrnydphfiAGSLDEAYLDItevc----------------------------------------------- 210 thale cress
AAW46481  293 KASKAVKEVLvqydenlmMASLDEGYLNItpym----------------------------------------------- 325 Cryptococcus neofo...
EAK83015  221 QASQKVMAIFeqydenlaKASLDEAYLDIteyv----------------------------------------------- 253 Ustilago maydis 521
EAN79815  208 EESNTVRRIVaeydpnftSLGLDELTLEVsayie---------------------------------------------- 241 Trypanosoma brucei
EAN87784  190 AEAAVVRGIAaaydpnftSVGLDELTMEVtayl----------------------------------------------- 222 Trypanosoma cruzi
CAJ05435  218 REAARVHSIAsrydaqfvSVGLDELTMDVtkyl----------------------------------------------- 250 Leishmania major
CAJ05431  306 VESAKFKGVVreydpdaqLLGMDEVMMCLddylahhhv------------------------------------------ 343 Leishmania major
AAN15780  176 AVSKEVKEILadydpnfmAMSLDEAYLNItkhleerqnwpedkrryfikmgssvendnpgkevnklsehersispllfee 255 human
O74944    204 IKSKEIQNVLaqydsnlcPASIDEFYMNLtshl----------------------------------------------- 236 fission yeast
Feature 1                                                                                     
1JX4_A    115 ----------------------------vrdYREAYNLGLEIKNKILEKek----iTVTVGISk----NKVFAKIAADXA 158 Sulfolobus solfata...
AAS91582  211 ----------------------------rerGLSGGEIAEELRSSVYSEtg----lTCSAGVAa----NRLLAKVCSDIN 254 thale cress
AAW46481  326 ----------------------------sthNMTASEVVTEIRAQVEEKts----lTISAGIAa----NRMLAKICSDKN 369 Cryptococcus neofo...
EAK83015  254 ----------------------------eqnASSIDQVVQQLRNQVRSHtq----lTVSVGIAp----NTMLAKISSDRN 297 Ustilago maydis 521
EAN79815  242 ---------------------------rfegTKTAEDVASELRVRVFGEtk----lTASAGIGp----TAALAKIASNIN 286 Trypanosoma brucei
EAN87784  223 ---------------------------qqhpGMTAGDVASEFRARVFAEtq----lTASAGIGp----TATLAKIASNYE 267 Trypanosoma cruzi
CAJ05435  251 ---------------------------qefpAVSASDIAHDFRDEVFLKtq----lTSSGGIGp----TSILAKIASNVN 295 Leishmania major
CAJ05431  344 -----------------------dvtthagrFDVAERVIEECRRRIAEAtg----lTVSAGIAp----TPTLAKMASNYK 392 Leishmania major
AAN15780  256 spsdvqppgdpfqvnfeeqnnpqilqnsvvfGTSAQEVVKEIRFRIEQKtt----lTASAGVRissfpNEEDRKHQQRSI 331 human
O74944    237 ---------------------------rlqeLAFTVENITMVVEKIRKQvheetgvTVSCGIAa----NKLLAKIASNKR 285 fission yeast
Feature 1     #                                                                               
1JX4_A    159 KPNGIKVIdd----------eeVKRLIRELdi--------adVPGIGNITAEKLKKLGINklVDTLSIEFDklkg----- 215 Sulfolobus solfata...
AAS91582  255 KPNGQFVLqnd--------rstVMTFVSFLpv--------rkIGGIGKVTEHILKDALGIktCEEMVQKGSllya----- 313 thale cress
AAW46481  370 KPNGHFELafd--------ratIVRFMRDLpv--------rnIPGFGRVTERCLEGLGIQtcGDIYEKRVDlllm----- 428 Cryptococcus neofo...
EAK83015  298 KPDGQFRIqpd--------rkvIVDFMRNLpc--------rkIPGIGRVNERILESLGVTtcGEIWDKRVElwl------ 355 Ustilago maydis 521
EAN79815  287 KPNGQHDLnlht-------redVMTYVRDLgl--------rsVPGIGKVTEALLKGLGITtlSDIYNRRVElcyi----- 346 Trypanosoma brucei
EAN87784  268 KPNGQHELrlrt-------rqdVMEFMKDLpv--------rtVPGIGPVQDAILRVLGIRtcGCMLRKKGLlcfl----- 327 Trypanosoma cruzi
CAJ05435  296 KPNGQHEItllt-------reeVINYVRDIpl--------rkIPGIGYAQEMTLGALHIHtcGGLLEHKYLlayl----- 355 Leishmania major
CAJ05431  393 KPNGQFAVrlfs-------reaVINYLASIpv--------rqVPGIGKSRESILAGLGIRtlGEVYEQRHRlfyi----- 452 Leishmania major
AAN15780  332 IGFLQAGNqalsatectlektdKDKFVKPLemshkksffdkkRSERKWSHQDTFKCEAVNkqSFQTSQPFQvlkkkmnen 411 human
O74944    286 KPNNQFFIpfd--------eigISKFMNDLpv--------reVSGIGRVLEQQLLGLEIKtcGDIQRNLVIlsyi----- 344 fission yeast
Feature 1                                                                                     
1JX4_A    216 --------xigeAKAKYLISLARDEYnepir---------------------------trvrKSIGRIVTXKRNsrnle- 259 Sulfolobus solfata...
AAS91582  314 --------lfsqSSADFFLSVGLGLGgtntp--------------------------qvrsrKSISSERTFAATgderl- 358 thale cress
AAW46481  429 ---------dhwFGFRGLCRAYLGIAdntvap------------------------grreerRSVGVERTFRDKtdded- 474 Cryptococcus neofo...
EAK83015  356 ---------sfdGKIEWLIKAHLGIGntvvep------------------------skreerKSVGREHTFSPTsdtka- 401 Ustilago maydis 521
EAN79815  347 ---------fteKTYCFLLGASIGIMqwpdmcsilga---------------siddgtgvgrKSVGCERTFKTFqnk--- 399 Trypanosoma brucei
EAN87784  328 ---------fpeKTFRFYLSAGLGVVrsnadlm-----------------------rsdgtqKKMGHEITFKRRlks--- 372 Trypanosoma cruzi
CAJ05435  356 ---------freKTLAHYLSVGLGLAetfslr-------------------------khqarQSVGKETSFSEPlpspea 401 Leishmania major
CAJ05431  453 ---------ltrKTYEFLLASSIGIGgmydsretapsssagattgktvaamdgasneddwgrKSVGHERTFYKLmnrmal 523 Leishmania major
AAN15780  412 leisensddcqiLTCPVCFRAQGCISlealnkhvdec---------------ldgpsisenfKMFSCSHVSATKvnkken 476 human
O74944    345 ---------flpKSFQNLLRCSYGFGttilde------------------------ygeskrKTIGSEATFSSNlsspsi 391 fission yeast
Feature 1                                                                                     
1JX4_A    260 ---------eikpyLFRAIEESYYKldk--------riPKAIHVVAVTed--------------ldIVSRGRTFphgi-s 307 Sulfolobus solfata...
AAS91582  359 ----------lyskLDELAEMLSHDmkke------gltARTLTLKLKTas--------------feIRSRAVSLqrytcs 408 thale cress
AAW46481  475 ----------imatLIDIVEELGKDldrl------qyaGKTVTVKYKTrak-------------siPKYISSATd----- 520 Cryptococcus neofo...
EAK83015  402 ----------lldlLKESAQRVEQDlarl------dfkAKTITLVAKRdnf------------qrfSRARTSTRlvhr-- 451 Ustilago maydis 521
EAN79815  400 ------------eeLQEMVDFLVDYsydelk--khelmCRQVSLKIRWnsy------------rhqQYTKNLTQysdd-- 451 Trypanosoma brucei
EAN87784  373 -----------eaeLKQIVLEVLVAvhntll--lrrvaAQRVTLLMKRrt--------------feNHQFSLTLgeatnd 425 Trypanosoma cruzi
CAJ05435  402 f-------trlfrkLLEQCHVRCVRdh---------lqPRKMTLVLKYrtydt---------eqfsVTLPSHTNdl---- 452 Leishmania major
CAJ05431  524 q-------aiayknLRRSQETLVEEg-----------lLCSQVVLKLKhhs-------------fhVKQHSKSLnvytdd 572 Leishmania major
AAN15780  477 vpasslcekqdyeaHPKIKEISSVDcialvdtidnsskAESIDALSNKhskeecsslpsksfniehCHQNSSSTv----- 551 human
O74944    392 i------eyklrllVQNVSENLQKRglv--------tnSIAIKYKTSEf----------------qVHTKQKSIgqfihs 441 fission yeast
Feature 1                                       
1JX4_A    308 ketAYSESVKLLQKILeed-erkIRRIGVRFSKF 340 Sulfolobus solfataricus
AAS91582  409 sddILKHATKLLKAELpv----sVRLIGLRMSQF 438 thale cress
AAW46481  521 ---ILPIAQELLKKELpl----rIRLLGVRLSTL 547 Cryptococcus neoformans var. neoformans JEC21
EAK83015  452 aeeLYDITSSLLMQEIeregaisLRLIGVRVTQL 485 Ustilago maydis 521
EAN79815  452 satLRRAVDELMLPHAaky--seMRLLGVRFLDL 483 Trypanosoma brucei
EAN87784  426 faaLREATRKLLQPHLtsf--dkFRLVGVRLGKL 457 Trypanosoma cruzi
CAJ05435  453 -kvWLEASQKLLEPHLlhy--aeLRLIGVRLQRF 483 Leishmania major
CAJ05431  573 hevLRRALDELLLPVMddf--aeFRLLGVRLEKL 604 Leishmania major
AAN15780  552 --sLENEDVGSFRQEYr-----qPYLCEVKTGQA 578 human
O74944    442 esdLLKPALQLLRQSYpm----tIRLLGVRATKL 471 fission yeast

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