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: 2-Oct-2020
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:
Feature 1                                                                                     
3GDX_A      4 GGITDMLTELANFEKNvsQAIHKYNAYRKAASVIAKYPHKIKSGAEakKLPGVGTKIAEKIDEFLATGKLRKLEKIrqdd 83  human
2IHM_A     18 TLLSEALETLAEAAGFe-ANEGRLLSFSRAASVLKSLPCPVASLSQlhGLPYFGEHSTRVIQELLEHGTCEEVKQVrcse 96  house mouse
1KDH_A     19 QLFTDALDILAENDELr-ENEGSCLAFMRASSVLKSLPFPITSMKDteGIPCLGDKVKSIIEGIIEDGESSEAKAVlnde 97  house mouse
1KEJ_A     19 QLFTDALDILAENDELr-ENEGSCLAFMRASSVLKSLPFPITSMKDteGIPCLGDKVKSIIEGIIEDGESSEAKAVlnde 97  house mouse
2BPF_A     13 GGITDMLVELANFEKNvsQAIHKYNAYRKAASVIAKYPHKIKSGAEakKLPGVGTKIAEKIDEFLATGKLRKLEKIrqdd 92  Norway rat
NP_984822 136 AKVACALQQLAERCRLq-GEAFRNRAYLLAREAVLELPYSIQTYEQarSLPNVGDGIAQKIALLAAGGSVPGLELEltp- 213 Ashbya gossypii AT...
549065    166 KKFTDAFEIMAENYEFk-ENEIFCLEFLRAASVLKSLPFPVTRMKDiqGLPCMGDRVRDVIEEIIEEGESSRAKDVlnde 244 chicken
CAC18211  244 EPFIEELMKIRTARTLl-GDKIGVRAYSSAIAALISYPYPLQSAFEvaRLPGCGLKIAQLYQEFREQGELQEAKEDesdp 322 Neurospora crassa
XP_451480 148 YKLIKVLKSLEKRYKLq-NDTFRYLGYMKMIKILQNVRVKIESEEDa-IENGLSKGLSKKIPFLLKLGESGSELKMdt-- 223 Kluyveromyces lact...
P42118    162 RIFTDAFDILAEHFEFc-ENKGRTVAFLRASSLIKSLPFPITAMKEleGLPWLGDQMKGIIEEILEEGKSYKVLEVmnee 240 African clawed frog
Feature 1             # # ######  #                       #             #                     
3GDX_A     84 tsSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRkne--dkLNHHQRIGLKYFGDFeKRIPREEMLQMQDIVLNEVKkvd 161 human
2IHM_A     97 ryQTMKLFTQVFGVGVKTANRWYQEGLRTLDELReqp--qrLTQQQKAGLQYYQDLsTPVRRADAEALQQLIEAAVRqtl 174 house mouse
1KDH_A     98 ryKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQsdk-slrFTQMQKAGFLYYEDLvSCVNRPEAEAVSMLVKEAVVtfl 176 house mouse
1KEJ_A     98 ryKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQsdk-slrFTQMQKAGFLYYEDLvSCVNRPEAEAVSMLVKEAVVtfl 176 house mouse
2BPF_A     93 tsSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRkne--dkLNHHQRIGLKYFEDFeKRIPREEMLQMQDIVLNEVKkld 170 Norway rat
NP_984822 214 deRIVRYFAACHDVGPGRAQQWRALGFESFADVLraspqwrLPWAMLYGMRFYEDWqLRIPRDEVGEHAAVLEQCAPa-- 291 Ashbya gossypii AT...
549065    245 ryKSFKEFTSVFGVGVKTSEKWFRMGLRTVEEVKadk-tlkLSKMQRAGFLYYEDLvSCVSKAEADAVSSIVKNTVCtfl 323 chicken
CAC18211  323 rlAVLKLFHEIWGVAETTAREFYNKGWRDLDDIVeyg-wdtLTRVQQIGVKYYDEFqQKIARAEVESIANIILEHANkih 401 Neurospora crassa
XP_451480 224 seQTLLYFQECHGIGAFKSKQYVNMGYSTFEDLIp-----yMNWTQLTGLAFYEDWqLSIPREETMKHEAIIRKAMNevn 298 Kluyveromyces lact...
P42118    241 ryKSFKQFTSVFGVGLKTSDKWFRMGFRTLEEIKnek-elkLTKMQKCGLLYYEDItSYVSRAEAETTEQLIKSIVWkfv 319 African clawed frog
Feature 1             ##  # # #### #                                                          
3GDX_A    162 seYIATVCGSFRRGAESSGDMDVLLThpsftsestkqpkllhQVVEQLQkvhfitd------------------------ 217 human
2IHM_A    175 pgATVTLTGGFRRGKLQGHDVDFLIThpeegq----evgllpKVMSCLQsqglvlyhqyhrshlad-------------- 236 house mouse
1KDH_A    177 pdALVTMTGGFRRGKMTGHDVDFLITspeated--eeqqllhKVTDFWKqqglllycdilestfe--------------- 239 house mouse
1KEJ_A    177 pdALVTMTGGFRRGKMTGHDVDFLITspeated--eeqqllhKVTDFWKqqglllycdilestfe--------------- 239 house mouse
2BPF_A    171 peYIATVCGSFRRGAESSGDMDVLLThpnftsesskqpkllhRVVEQLQkvrfitd------------------------ 226 Norway rat
NP_984822 292 -gMSVVIAGSYSRGSTTCGDIDVVLYregcddpe-vladdltALVQRLVsigyvecplhlskrlq--------------- 354 Ashbya gossypii AT...
549065    324 pdALVTITGGFRRGKKIGHDIDFLITsp------------gqREDDELLhkglllycdiiestfv--------------- 376 chicken
CAC18211  402 pgFQMVIVGGYRRGKLASGDVDVVLShpdkaa----trgfveQIVVALEqsnyithtlilstantergq----------- 466 Neurospora crassa
XP_451480 299 enLCMEITGSYRRGQPRSGDIDIVVHmpgqndln-yisreleKVIIKLTetgyiicplnlnetlkslfqpwfhklfshfn 377 Kluyveromyces lact...
P42118    320 pdAIVTLTGGFRRGKKKGHDVDILITcark---------gkeKNILHNTmsvlknrglllfyniiest------------ 378 African clawed frog
Feature 1                                               # #                                   
3GDX_A    218 -----------------------------------tlskgetKFMGVCQlpsknd------------------------- 237 human
2IHM_A    237 --------------------------sahnlrqrsstmdvfeRSFCILGlpqpqqaala--------------------- 269 house mouse
1KDH_A    240 --------------------------kfkqpsrkvdaldhfqKCFLILKldhgrvhsek--------------------- 272 house mouse
1KEJ_A    240 --------------------------kfkqpsrkvdaldhfqKCFLILKldhgrvhsek--------------------- 272 house mouse
2BPF_A    227 -----------------------------------tlskgetKFMGVCQlpsend------------------------- 246 Norway rat
NP_984822 355 --------------------------plfdpavhslarglgvSVSGRLSekdtlarfysgvrlpgkapvppgapaipyva 408 Ashbya gossypii AT...
549065    377 --------------------------keqipsrhvdamdhfqKCFAILKlyqprvdnssynm------------------ 412 chicken
CAC18211  467 ----------------------epvawkgnekksgtgfdtldKALVVWQdphwttd------------------------ 500 Neurospora crassa
XP_451480 378 kpfdvkaydepvhkfycgaavtkyepdrikdadaltlkgndkKYKMDIGk------------------------------ 427 Kluyveromyces lact...
P42118    379 ------------------------fdetklpsrhvdaldhfqKCFTILKlpkrqmdignii------------------- 415 African clawed frog
Feature 1                       # #              ######  #                #                   
3GDX_A    238 -----------ekeypHRRIDIRLIPKDQYYCGVLYFTGSDiFNKNMRAHAL-EKGFTINEYTIRPlgvt-------gva 298 human
2IHM_A    270 ------galppcptwkAVRVDLVVTPSSQFPFALLGWTGSQfFERELRRFSRqEKGLWLNSHGLFDpe-----------q 332 house mouse
1KDH_A    273 ------sgqqegkgwkAIRVDLVMCPYDRRAFALLGWTGSRqFERDLRRYAThERKMMLDNHALYDrt-----------k 335 house mouse
1KEJ_A    273 ------sgqqegkgwkAIRVDLVMCPYDRRAFALLGWTGSRqFERDLRRYAThERKMMLDNHALYDrt-----------k 335 house mouse
2BPF_A    247 -----------eneypHRRIDIRLIPKDQYYCGVLYFTGSDiFNKNMRAHAL-EKGFTINEYTIRPlgvt-------gva 307 Norway rat
NP_984822 409 qdrelfaphasgsarpCRRLDLLTCKWSERGACLLYFIGNDtFNKALRTRAS-AQGMTLNQHGLFDks-----------s 476 Ashbya gossypii AT...
549065    413 ---skkcdmaevkdwkAIRVDLVITPFEQYAYALLGWTGSRqFGRDLRRYAThERKMMLDNHALYDkr-----------k 478 chicken
CAC18211  501 ---------ekknpipHRRVDIIISPWKTAGCAVLGWTSGTtFQRDLRRYCKkERSLKFDSSGIRSradgtwvdfesgpn 571 Neurospora crassa
XP_451480 428 ---------------tCRRVDFLLAEYQGLGATNVYFTGNNnFNKKCRTIAK-QKGYVLSNDGIYKd------------- 478 Kluyveromyces lact...
P42118    416 -----dphecerknwkAVRLDLVITPYEQYPYALLGWTGSRqFERDLRRYAThEKRMMLDNHGLYDkt-----------k 479 African clawed frog
Feature 1                                 
3GDX_A    299 GEPLPVDS--EKDIFDYIQWKYREPKDR 324 human
2IHM_A    333 KRVFHATS--EEDVFRLLGLKYLPPEQR 358 house mouse
1KDH_A    336 RVFLEAES--EEEIFAHLGLDYIEPWER 361 house mouse
1KEJ_A    336 RVFLEAES--EEEIFAHLGLDYIEPWER 361 house mouse
2BPF_A    308 GEPLPVDS--EQDIFDYIQWRYREPKDR 333 Norway rat
NP_984822 477 GACVESAD--EYRIMELLGFPRLEPTDE 502 Ashbya gossypii ATCC 10895
549065    479 RVFLKAGS--EEEIFAHLGLDYVEPWER 504 chicken
CAC18211  572 GEPAPDMLtaERRVFEGLGLEWRPPEER 599 Neurospora crassa
XP_451480 479 GQLIPVAD--EYEILDMIGVDKLKPTER 504 Kluyveromyces lactis NRRL Y-1140
P42118    480 NNFLKANN--EEDIFKQLGLDYLEPWER 505 African clawed frog

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