2WTF,1JX4,2ALZ,2AQ4


Conserved Protein Domain Family
PolY

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cd00424: PolY 
Click on image for an interactive view with Cn3D
Y-family of DNA polymerases
Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Statistics
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PSSM-Id: 176453
View PSSM: cd00424
Aligned: 13 rows
Threshold Bit Score: 245.348
Threshold Setting Gi: 15076198
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active siteDNA binding
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:1JX4_A; Sulfolobus solfataricus Y-family DNA polymerase binds 2',3'-Dideoxyadenosine-5'-diphosphate and Ca2+, defined using 4.0 A contacts
    View structure with Cn3D
  • Structure:2AQ4_A; Yeast Rev1 binds dCTP and Mg2+, defined using 4.0 A contacts
    View structure with Cn3D
  • Structure:2ALZ_A; Human DNA polymerase iota binds dCTP and Mg2+, defined using 4.0 A contacts
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1          ##  ##                                            #  #                       
2WTF_A       50 AHIDMNaFFAQVEQMRcgl---------skEDPVVCVqwns-------iiavSYAARKYGisrmDTIQEALKKCSnlipi 113 baker's yeast
1JX4_A        4 LFVDFDyFYAQVEEVLnps---------lkGKPVVVCvfsgrfedsgavataNYEARKFGvkagIPIVEAKKILPnavyl 74  Sulfolobus solfa...
2ALZ_A        7 VHVDLDcFYAQVEMISnpe---------lkDKPLGVQqkyl-------vvtcNYEARKLGvkklMNVRDAKEKCPqlvlv 70  human
2AQ4_A       55 FHIDFDcFFATVAYLCrsssfs---acdfkRDPIVVChgtkns----diascNYVARSYGikngMWVSQAEKMLPngikl 127 baker's yeast
ZP_00054570  16 LYLDFDgFFASCEQFAhph---------lrGKPIGVVpfagavn--tcviacSREAKKRGvsnvMMVKDALRLCPdlilq 84  Magnetospirillum...
ZP_00665306   6 VHLDIPnFYAVLEELRrpelkkrsmvlaepSARAIVQg-------------iNSNAGKEGiregMPLAHARRMCRrvlav 72  Syntrophobacter ...
ABA88983      6 LHVAVPdFDVALARAAdpg---------leSRPLAVAtgvser---allrcvSAEARSDGvqpgMSVYVARKCCPalhl- 72  Pelobacter carbi...
ZP_00957198  10 LYLDFDsFFASVEQYAdpr---------lrGRPVGVIpmqgarn--tciiaaSKEAKAKGassvMTVREAREAVPdmilv 78  Oceanicaulis ale...
ZP_01016567  10 LYLDFDgFFASVMQQAmph---------lrGKPVGVIpfdtasaqyttviacSKEAKARGvqnvMRVPEARAICPdivlv 80  Parvularcula ber...
ZP_01017982  14 LYIDFNaFFAAAAQHDepa---------laGRPVVITphrsey---ssaiavSYEARPFGirrgTKIREARHLCPavavr 81  Parvularcula ber...
ZP_01058405   5 GLVDCNnFYASCERVFqpe---------liERPLVVLsnndg-----cvvarSQEAKDLGipmgVPLFKIRNLVRdhgve 70  Roseobacter sp. ...
ZP_01092692   7 LWMDMNsYFASVEQQLrpe---------lrKQPVGVVpldtds---tciiaaSYDAKRSGvkvgTKVYDARRLCPgiqli 74  Blastopirellula ...
CAC47751     25 LSIHFPhLPTDRVARSrwgasw--lsrgrpDHPPVVFaakidna--mrlvalDTFAERIGlkrgQGAAEARAMCPsldvi 100 Sinorhizobium me...
Feature 1                                                                           ##          
2WTF_A      114 htavfkkgedfwqyhdgcgswvqdpakqisvedhkvslepYRRESRKALKIFksac----dlveRASIDEVFLDLgricf 189 baker's yeast
1JX4_A       75 p----------------------------------xrkevYQQVSSRIXNLLreys----ekieIASIDEAYLDIsdkvr 116 Sulfolobus solfa...
2ALZ_A       71 n---------------------------------gedltrYREMSYKVTELLeefs----pvveRLGFDENFVDLtemve 113 human
2AQ4_A      128 is-------------------------------lpytfeqFQLKSEAFYSTLkrlni--fnlilPISIDEAVCVRiipdn 174 baker's yeast
ZP_00054570  85 p----------------------------------qnpdlYRRAHNALLSEIamvi----pidaVKSIDELTCRLdpsqq 126 Magnetospirillum...
ZP_00665306  73 a----------------------------------pdlrfYREEHQQILKEFgffs----plveGAWPGHYFVDLtgtqr 114 Syntrophobacter ...
ABA88983     73 -------------------------------------lppQAELAQRATRVFgelaaccsplwePGSPGRFFIDLtgsrr 115 Pelobacter carbi...
ZP_00957198  79 d----------------------------------qkpdlYRRMHALMIAEIravl----pigaVKSIDELTCPLdgrai 120 Oceanicaulis ale...
ZP_01016567  81 m----------------------------------qrpdlFRWAHGALLNEIscei----pietVKSIDELCCTLtksdi 122 Parvularcula ber...
ZP_01017982  82 p----------------------------------arhdrYIRLHKELIGAIetvl----plgkVYSIDEATFRLdrtqa 123 Parvularcula ber...
ZP_01058405  71 vr--------------------------------ssnyalYGDLSERVMSILadsa----prseVYSIDECFLDLhhlav 114 Roseobacter sp. ...
ZP_01092692  75 k----------------------------------arpdvYVRMHHRLLASVekca----pierIYSIDEWTIRLlgadr 116 Blastopirellula ...
CAC47751    101 aad------------------------------paadqafLEALADWCDRYTpl--------vaLDGTDGLFLDItgcah 142 Sinorhizobium me...
Feature 1                                                                                       
2WTF_A      190 nmlmfdneyeltgdlklkdalsnireafiggnydinshlplipekikslkfegdvfnpegrdlitdwddvilalgsQVCK 269 baker's yeast
1JX4_A      117 d----------------------------------------------------------------------yreayNLGL 126 Sulfolobus solfa...
2ALZ_A      114 krlqqlqsdelsavtvsg------------------------------------hvynnqsinlldvlhirllvgsQIAA 157 human
2AQ4_A      175 ih-------------------------------------------------------------------ntntlnaRLCE 187 baker's yeast
ZP_00054570 127 ------------------------------------------------------------------------qdplAVGE 134 Magnetospirillum...
ZP_00665306 115 l----------------------------------------------------------------------lgpgpDVAC 124 Syntrophobacter ...
ABA88983    116 l----------------------------------------------------------------------lgatlDVAA 125 Pelobacter carbi...
ZP_00957198 121 ------------------------------------------------------------------------adpeGVSN 128 Oceanicaulis ale...
ZP_01016567 123 ------------------------------------------------------------------------gdpqGLAR 130 Parvularcula ber...
ZP_01017982 124 s----------------------------------------------------------------------pdrarIQAE 133 Parvularcula ber...
ZP_01058405 115 ------------------------------------------------------------------------psltEWCL 122 Roseobacter sp. ...
ZP_01092692 117 q----------------------------------------------------------------------leqarRLAY 126 Blastopirellula ...
CAC47751    143 ------------------------------------------------------------------------lhggEKAL 150 Sinorhizobium me...
Feature 1                                         #                                             
2WTF_A      270 GIRDSIKDIlg--yTTSCGLSsTKNVCKLASNYKKPDAQtivkndclldf----ldcgkfeitsFWTLGGVLGKELIDVL 343 baker's yeast
1JX4_A      127 EIKNKILEKek--iTVTVGISkNKVFAKIAADXAKPNGIkviddeevkr------lireldiadVPGIGNITAEKLKKLG 198 Sulfolobus solfa...
2ALZ_A      158 EMREAMYNQlg--lTGCAGVAsNKLLAKLVSGVFKPNQQtvllpescqh-----lihslnhikeIPGIGYKTAKCLEALG 230 human
2AQ4_A      188 EIRQEIFQGtn-gcTVSIGCSdSLVLARLALKMAKPNGYnitfksnlse-----efwssfklddLPGVGHSTLSRLESTF 261 baker's yeast
ZP_00054570 135 AIKARLLKLvgpwiKCSLGYAaNRQLAKMACKAGKPDGNmlwhpddmpg------pllkisirdVPGIGKRILHRLWDAG 208 Magnetospirillum...
ZP_00665306 125 RMERHLATQrr--lRARIGLAaNKLVSQVASTCIVPGDLncifpggets------flaplpvtsLPGVGAVTASRLADFN 196 Syntrophobacter ...
ABA88983    126 RLERDIVERlr--lSATCGMAgNKLVARIAADYLHRPGIcdvlrgsesc------figpltvstLPGVGSVRTGRLLADL 197 Pelobacter carbi...
ZP_00957198 129 AIKARIAAQtdgvvTCSIGMApNRFLAKMACKLGKPDGLtiwrpedlpg------pllkrpldeAPGIGSSMRKRLLKAG 202 Oceanicaulis ale...
ZP_01016567 131 RLKSFIAENigphiTCSIGYAaNRLLAKMACKMDKPNGVtiwrpedmpr------plqdlplteVPGIGGRMEKRLAAAG 204 Parvularcula ber...
ZP_01017982 134 AVKSVIADRigpsfRNSIGIAqTPLLAKLAAGLQKPDGLtvlmmedlpg------rlsslalsdLPGIGPNMAQRLERSG 207 Parvularcula ber...
ZP_01058405 123 DLRQQVRAWtg--iPVSIGIGpTKTLAKLANKLAKSSPRtggvldlvhhpqwrepalrkvavgdVWGIGRRWSQMLEAQN 200 Roseobacter sp. ...
ZP_01092692 127 RIKRHVAHEiglwmSCSIGIAaTRLLAKIAAGLEKPHGLtalpqealpe------riehlpltkLNGVNVGIERRLHQHG 200 Blastopirellula ...
CAC47751    151 ISDVLSRLFsl-gvEARATVSsAAGLSWAVTRYGDADVIapgdgdpv----------laplpvaALRLPADTAAALERVG 219 Sinorhizobium me...
Feature 1                                                                                       
2WTF_A      344 DlphensikhiretwpdnagqlkefldakvkqsdydrstsnidplktaDLAEKLFKLSRGryglpl-------ssrpvvK 416 baker's yeast
1JX4_A      199 Inklvdtlsie---------------------------fdklkgxigeAKAKYLISLARDeynepi--------rtrvrK 243 Sulfolobus solfa...
2ALZ_A      231 Insvrdlqtfs---------------------------pkilekelgiSVAQRIQKLSFGednspv-------ilsgppQ 276 human
2AQ4_A      262 Dsphslndlrkry------------------------tldalkasvgsKLGMKIHLALQGqddeeslkilydpkevlqrK 317 baker's yeast
ZP_00054570 209 Ivemtdllnaq---------------------------pkqmraiwgnVTGERLWYALHGydiqa---------qaserG 252 Magnetospirillum...
ZP_00665306 197 Irrigqlaals----------------------------lealcgvfgKMGSRLFNVARGidptpv-------lpsresP 241 Syntrophobacter ...
ABA88983    198 Nlrrieqvaal---------------------------svaqlepvcgPFAALLQQRARGidpspv-------cpprrsS 243 Pelobacter carbi...
ZP_00957198 203 Vadmkalwalq---------------------------pkqmralwrnVAGERFWYALHGyavqa---------epakrR 246 Oceanicaulis ale...
ZP_01016567 205 Vnqmeglldlq---------------------------pkqaralwgnVTGERLWYALHGyalka---------eptgrG 248 Parvularcula ber...
ZP_01017982 208 Vtnidalwala---------------------------pkqaraiwrsVQGERFWYAFHGyevpe---------patkkG 251 Parvularcula ber...
ZP_01058405 201 Ihtahdlsras----------------------------dgwvrkrmgIVGLRTVHELRGiachdld------tqpdpkQ 246 Roseobacter sp. ...
ZP_01092692 201 Vtnirelwnln---------------------------rdemtrawgsISGSRWWAGLHGvdepe---------pptrrQ 244 Blastopirellula ...
CAC47751    220 Lkqigdlleap----------------------------raplarrfgSSLLLRLDQARGfedepl-------sprlpvP 264 Sinorhizobium me...
Feature 1                                                                                       
2WTF_A      417 SMMSNKNLRGKscnsiv---dciswLEVFCAELTSRiqdleqeynkiviPRTVSISLKTks-------------yeVYRK 480 baker's yeast
1JX4_A      244 SIGRIVTXKRNsrnle----eikpyLFRAIEESYYKldk--------riPKAIHVVAVTed-------------ldIVSR 298 Sulfolobus solfa...
2ALZ_A      277 SFSEEDSFKKCsseve-----aknkIEELLASLLNRvcqd------grkPHTVRLIIRRysse---------khygRESR 336 human
2AQ4_A      318 SLSIDINWGIRfknit----qvdlfIERGCQYLLEKlnein----kttsQITLKLMRRCkdapieppkymgmgrcdSFSR 389 baker's yeast
ZP_00054570 253 MYGHGRVMPPDhrtma----avkpiSRLLLVKAARRmrrd------gwsAGRLFLWLGMwddsw-------sgsayLPAI 315 Magnetospirillum...
ZP_00665306 242 RLVVAHSLERDeidrd----rlealLFQQVEEAGWAlrsh------nrhPTRFVLEIRYad--------------gITAR 297 Syntrophobacter ...
ABA88983    244 AIIEETVLPRAdnd--------dmaVRAALGRLAEScglrlr--elgrgTTCLRLQVRYvdg-----------lseERTD 302 Pelobacter carbi...
ZP_00957198 247 MYGHGRVLPPShrtwp----saydcARLLTVKAARRmrrd------grtAGRMGLWLRHieggw-------sgelpLHSA 309 Oceanicaulis ale...
ZP_01016567 249 MYGHGRVLPPEwrnld----kaydcARLLLIKAARRmrrd------rfyTNRLWVWLDLrkgaw-------vqcrdIPSA 311 Parvularcula ber...
ZP_01017982 252 MVGHSRVLTSGlrtak----garpvARALLLKAAARlram------drlATRLTLTLKDeqgrki------afeerFDLS 315 Parvularcula ber...
ZP_01058405 247 TTCCSRSFGRVisekq----dlrsaVITFAERAAGKvraa------nqvAGALQVFVSTd----------------RFNK 300 Roseobacter sp. ...
ZP_01092692 245 SMSHGNVLDPQfrtad----gahciLVKLICKLAQRlrrs------gyyANVLQLSLKDvrggrf------etktpIPCL 308 Blastopirellula ...
CAC47751    265 SFSAERRLAEPlqdeehileltrhlARDVRSSLERHge----------gGRLFELLLFRvdgrvfr----vrahaaVPLN 330 Sinorhizobium me...
Feature 1                                                              
2WTF_A      481 SGPVaykgin-------fqsheLLKVGIKFVtdldikg-knksyypLTKLSMTIT 527 baker's yeast
1JX4_A      299 GRTFphgi----------sketAYSESVKLLqkile-----ederkIRRIGVRFS 338 Sulfolobus solfataricus
2ALZ_A      337 QCPIpshviqklgtgnydvmtpMVDILMKLFrnmvnv----kmpfhLTLLSVCFC 387 human
2AQ4_A      390 SSRLgiptn---------efgiIATEMKSLYrtlgc------ppmeLRGLALQFN 429 baker's yeast
ZP_00054570 316 SDDPg-----------------ILDALEEIWakarad---lprravIARIGVTLG 350 Magnetospirillum magnetotacticum MS-1
ZP_00665306 298 SAHAlfspai-------hadrrLFRVILPVFrqlfn------rriaLRRIVLELS 339 Syntrophobacter fumaroxidans MPOB
ABA88983    303 SFTApraf-----------dleLMHAADHLLqrtw--------qrrVRLRALRLG 338 Pelobacter carbinolicus DSM 2380
ZP_00957198 310 RTDRd-----------------CLKALDTLWaaaqra----dprarPMRAGMYLA 343 Oceanicaulis alexandrii HTCC2633
ZP_01016567 312 HDDKa-----------------ILSALDILWekarddl--arhkieIVRVGVTLS 347 Parvularcula bermudensis HTCC2503
ZP_01017982 316 TDSTt-----------------FLRALDRLWeraleq---vpelrrGARLGSVSI 350 Parvularcula bermudensis HTCC2503
ZP_01058405 301 AAPQygsaatvr---falptsdALHIVCAASralerv---wrggfaYRKAGVLLL 349 Roseobacter sp. MED193
ZP_01092692 309 QDTPs-----------------LLLQFEKLWksrpls----ntpllKVDVCVSDL 342 Blastopirellula marina DSM 3645
CAC47751    331 DAVR------------------IAALFRERLqavhddldagygfeiVRLSVLRSE 367 Sinorhizobium meliloti

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