3GDX,2IHM,1KDH,1KEJ,2W9M,1RZT,2BPF


Conserved Protein Domain Family
NT_POLXc

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cd00141: NT_POLXc 
Click on image for an interactive view with Cn3D
Nucleotidyltransferase (NT) domain of family X DNA Polymerases.
X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.
Statistics
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PSSM-Id: 143386
View PSSM: cd00141
Aligned: 51 rows
Threshold Bit Score: 199.344
Threshold Setting Gi: 223365736
Created: 1-Nov-2000
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 32 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:The active site annotation includes NTP- and primer-binding residues, and the binding site for two magnesium ions (the nucleotide binding ion, and the catalytic ion).
  • Structure:2BPF_A, Rat DNA Pol beta bound with a primer, ddCTP, and 2 magnesium ions; contacts determined at 4A.
    View structure with Cn3D
  • Citation:PMID 7516581
  • Structure:2IHM_A, Mouse Pol mu bound with ddTTP, an upstream primer of a gapped primer-template duplex, and metal ions; contacts determined at 4A.
    View structure with Cn3D
  • Comment:In 2IHM_A, the catalytic site is occupied by a Na+ ion.
  • Structure:1KDH_A, mouse TdT bound with primer ssDNA, contacts at 4A.
    View structure with Cn3D
  • Structure:1KEJ_A, mouse TdT bound with ddATP and metal ions, contacts at 4A.
    View structure with Cn3D
  • Comment:For 1KEJ_A, Co2+ ions were used in place of Mg2+ ions.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
3GDX_A        4 GGITDMLTELANFEKNvsQAIHKYNAYRKAASVIAKYPHKIKSGAEakKLPGVGTKIAEKIDEFLATGKLRKLEKIrqdd 83
2IHM_A       18 TLLSEALETLAEAAGFe-ANEGRLLSFSRAASVLKSLPCPVASLSQlhGLPYFGEHSTRVIQELLEHGTCEEVKQVrcse 96
1KDH_A       19 QLFTDALDILAENDELr-ENEGSCLAFMRASSVLKSLPFPITSMKDteGIPCLGDKVKSIIEGIIEDGESSEAKAVlnde 97
1KEJ_A       19 QLFTDALDILAENDELr-ENEGSCLAFMRASSVLKSLPFPITSMKDteGIPCLGDKVKSIIEGIIEDGESSEAKAVlnde 97
2BPF_A       13 GGITDMLVELANFEKNvsQAIHKYNAYRKAASVIAKYPHKIKSGAEakKLPGVGTKIAEKIDEFLATGKLRKLEKIrqdd 92
gi 45190568 136 AKVACALQQLAERCRLq-GEAFRNRAYLLAREAVLELPYSIQTYEQarSLPNVGDGIAQKIALLAAGGSVPGLELEltp- 213
gi 549065   166 KKFTDAFEIMAENYEFk-ENEIFCLEFLRAASVLKSLPFPVTRMKDiqGLPCMGDRVRDVIEEIIEEGESSRAKDVlnde 244
gi 11595591 244 EPFIEELMKIRTARTLl-GDKIGVRAYSSAIAALISYPYPLQSAFEvaRLPGCGLKIAQLYQEFREQGELQEAKEDesdp 322
gi 50303085 148 YKLIKVLKSLEKRYKLq-NDTFRYLGYMKMIKILQNVRVKIESEEDa-IENGLSKGLSKKIPFLLKLGESGSELKMdt-- 223
gi 1174629  162 RIFTDAFDILAEHFEFc-ENKGRTVAFLRASSLIKSLPFPITAMKEleGLPWLGDQMKGIIEEILEEGKSYKVLEVmnee 240
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               # # ######  #                       #             #                     
3GDX_A       84 tsSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRkne--dkLNHHQRIGLKYFGDFeKRIPREEMLQMQDIVLNEVKkvd 161
2IHM_A       97 ryQTMKLFTQVFGVGVKTANRWYQEGLRTLDELReqp--qrLTQQQKAGLQYYQDLsTPVRRADAEALQQLIEAAVRqtl 174
1KDH_A       98 ryKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQsdk-slrFTQMQKAGFLYYEDLvSCVNRPEAEAVSMLVKEAVVtfl 176
1KEJ_A       98 ryKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQsdk-slrFTQMQKAGFLYYEDLvSCVNRPEAEAVSMLVKEAVVtfl 176
2BPF_A       93 tsSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRkne--dkLNHHQRIGLKYFEDFeKRIPREEMLQMQDIVLNEVKkld 170
gi 45190568 214 deRIVRYFAACHDVGPGRAQQWRALGFESFADVLraspqwrLPWAMLYGMRFYEDWqLRIPRDEVGEHAAVLEQCAPa-- 291
gi 549065   245 ryKSFKEFTSVFGVGVKTSEKWFRMGLRTVEEVKadk-tlkLSKMQRAGFLYYEDLvSCVSKAEADAVSSIVKNTVCtfl 323
gi 11595591 323 rlAVLKLFHEIWGVAETTAREFYNKGWRDLDDIVeyg-wdtLTRVQQIGVKYYDEFqQKIARAEVESIANIILEHANkih 401
gi 50303085 224 seQTLLYFQECHGIGAFKSKQYVNMGYSTFEDLIp-----yMNWTQLTGLAFYEDWqLSIPREETMKHEAIIRKAMNevn 298
gi 1174629  241 ryKSFKQFTSVFGVGLKTSDKWFRMGFRTLEEIKnek-elkLTKMQKCGLLYYEDItSYVSRAEAETTEQLIKSIVWkfv 319
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               ##  # # #### #                                                          
3GDX_A      162 seYIATVCGSFRRGAESSGDMDVLLThpsftsestkqpkllhQVVEQLQkvhfitd------------------------ 217
2IHM_A      175 pgATVTLTGGFRRGKLQGHDVDFLIThpeegq----evgllpKVMSCLQsqglvlyhqyhrshlad-------------- 236
1KDH_A      177 pdALVTMTGGFRRGKMTGHDVDFLITspeated--eeqqllhKVTDFWKqqglllycdilestfe--------------- 239
1KEJ_A      177 pdALVTMTGGFRRGKMTGHDVDFLITspeated--eeqqllhKVTDFWKqqglllycdilestfe--------------- 239
2BPF_A      171 peYIATVCGSFRRGAESSGDMDVLLThpnftsesskqpkllhRVVEQLQkvrfitd------------------------ 226
gi 45190568 292 -gMSVVIAGSYSRGSTTCGDIDVVLYregcddpe-vladdltALVQRLVsigyvecplhlskrlq--------------- 354
gi 549065   324 pdALVTITGGFRRGKKIGHDIDFLITsp------------gqREDDELLhkglllycdiiestfv--------------- 376
gi 11595591 402 pgFQMVIVGGYRRGKLASGDVDVVLShpdkaa----trgfveQIVVALEqsnyithtlilstantergq----------- 466
gi 50303085 299 enLCMEITGSYRRGQPRSGDIDIVVHmpgqndln-yisreleKVIIKLTetgyiicplnlnetlkslfqpwfhklfshfn 377
gi 1174629  320 pdAIVTLTGGFRRGKKKGHDVDILITcark---------gkeKNILHNTmsvlknrglllfyniiest------------ 378
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                 # #                                   
3GDX_A      218 -----------------------------------tlskgetKFMGVCQlpsknd------------------------- 237
2IHM_A      237 --------------------------sahnlrqrsstmdvfeRSFCILGlpqpqqaala--------------------- 269
1KDH_A      240 --------------------------kfkqpsrkvdaldhfqKCFLILKldhgrvhsek--------------------- 272
1KEJ_A      240 --------------------------kfkqpsrkvdaldhfqKCFLILKldhgrvhsek--------------------- 272
2BPF_A      227 -----------------------------------tlskgetKFMGVCQlpsend------------------------- 246
gi 45190568 355 --------------------------plfdpavhslarglgvSVSGRLSekdtlarfysgvrlpgkapvppgapaipyva 408
gi 549065   377 --------------------------keqipsrhvdamdhfqKCFAILKlyqprvdnssynm------------------ 412
gi 11595591 467 ----------------------epvawkgnekksgtgfdtldKALVVWQdphwttd------------------------ 500
gi 50303085 378 kpfdvkaydepvhkfycgaavtkyepdrikdadaltlkgndkKYKMDIGk------------------------------ 427
gi 1174629  379 ------------------------fdetklpsrhvdaldhfqKCFTILKlpkrqmdignii------------------- 415
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                         # #              ######  #                #                   
3GDX_A      238 -----------ekeypHRRIDIRLIPKDQYYCGVLYFTGSDiFNKNMRAHAL-EKGFTINEYTIRPlgvt-------gva 298
2IHM_A      270 ------galppcptwkAVRVDLVVTPSSQFPFALLGWTGSQfFERELRRFSRqEKGLWLNSHGLFDpe-----------q 332
1KDH_A      273 ------sgqqegkgwkAIRVDLVMCPYDRRAFALLGWTGSRqFERDLRRYAThERKMMLDNHALYDrt-----------k 335
1KEJ_A      273 ------sgqqegkgwkAIRVDLVMCPYDRRAFALLGWTGSRqFERDLRRYAThERKMMLDNHALYDrt-----------k 335
2BPF_A      247 -----------eneypHRRIDIRLIPKDQYYCGVLYFTGSDiFNKNMRAHAL-EKGFTINEYTIRPlgvt-------gva 307
gi 45190568 409 qdrelfaphasgsarpCRRLDLLTCKWSERGACLLYFIGNDtFNKALRTRAS-AQGMTLNQHGLFDks-----------s 476
gi 549065   413 ---skkcdmaevkdwkAIRVDLVITPFEQYAYALLGWTGSRqFGRDLRRYAThERKMMLDNHALYDkr-----------k 478
gi 11595591 501 ---------ekknpipHRRVDIIISPWKTAGCAVLGWTSGTtFQRDLRRYCKkERSLKFDSSGIRSradgtwvdfesgpn 571
gi 50303085 428 ---------------tCRRVDFLLAEYQGLGATNVYFTGNNnFNKKCRTIAK-QKGYVLSNDGIYKd------------- 478
gi 1174629  416 -----dphecerknwkAVRLDLVITPYEQYPYALLGWTGSRqFERDLRRYAThEKRMMLDNHGLYDkt-----------k 479
                       410       420
                ....*....|....*....|....*...
Feature 1                                   
3GDX_A      299 GEPLPVDS--EKDIFDYIQWKYREPKDR 324
2IHM_A      333 KRVFHATS--EEDVFRLLGLKYLPPEQR 358
1KDH_A      336 RVFLEAES--EEEIFAHLGLDYIEPWER 361
1KEJ_A      336 RVFLEAES--EEEIFAHLGLDYIEPWER 361
2BPF_A      308 GEPLPVDS--EQDIFDYIQWRYREPKDR 333
gi 45190568 477 GACVESAD--EYRIMELLGFPRLEPTDE 502
gi 549065   479 RVFLKAGS--EEEIFAHLGLDYVEPWER 504
gi 11595591 572 GEPAPDMLtaERRVFEGLGLEWRPPEER 599
gi 50303085 479 GQLIPVAD--EYEILDMIGVDKLKPTER 504
gi 1174629  480 NNFLKANN--EEDIFKQLGLDYLEPWER 505

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