2FAQ,2FAR,2IRX,2IRY


Conserved Protein Domain Family
LigD_Pol_like

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cd04861: LigD_Pol_like 
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LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nucleotide additions to blunt-end duplex DNA; it preferentially adds single ribonucleotides at blunt DNA ends. PaeLigD Pol adds a correctly paired rNTP to the DNA primer termini more rapidly than it does a correctly paired dNTP; it has higher infidelity as an RNA polymerase than it does as a DNA polymerase, which is in keeping with the mutagenic property of NHEJ-mediated DNA DSB repair. The MtLigD Pol domain similarly is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap.
Statistics
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PSSM-Id: 240131
Aligned: 78 rows
Threshold Bit Score: 247.42
Created: 3-Nov-2006
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
nucleotide
Conserved site includes 17 residues -Click on image for an interactive view with Cn3D
Feature 1:nucleotide binding site [chemical binding site]
Evidence:
  • Structure:2FAQ_A, Pseudomonas aeruginosa LigD Polymerase domain, contacts with ATP and two manganese ions at 3.5 Angstrom
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  • Structure:2FAR_A, Pseudomonas aeruginosa LigD Polymerase domain, contacts with dATP and two manganese ions at 3.5 Angstrom
    View structure with Cn3D
  • Structure:2IRY, Mycobacterium tuberculosis ligase D Pol domain, bound with dGTP and manganese, contacts at 3.5 Angstrom
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  • Structure:2IRX_A, Mycobacterium tuberculosis ligase D Pol domain, bound with GTP and manganese, contacts at 3.5 Angstrom
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                 #               # #                                   
2FAQ_A       35 KLELAEFHARYADlLLRDLRERPVSLVRGPDGig----geLFFQKHAArlkIP-GIVQLDpald--pghpPLLQirSAEA 107 Pseudomonas aeru...
ZP_01170763 340 KIDFIHYLREISPyMLPFLKDRLLTVIRYPHGif----gePFYQKNAPd-yTPeFVETKMsd------giNYIVcnNLKT 408 Bacillus sp. NRR...
ZP_01575281  34 KLEYVKTMTKLAPfLIKYSKHRMLTSIRYPHGin----dkSFFQKEKPq-gTPeWVETVEfn------qkNYINlnSAAT 102 Clostridium cell...
NP_243075   339 KIDYLYYLQEVAPaMLPFLIDRPLTVIRYPHGvrsntereAFYQKNCPd-yAPsFVKTVRld------eiRYIVcnDIQT 411 Bacillus halodur...
NP_693956   328 KQDLLVYIREISPwMLPFLRQKALTIIRCPDGit----keSFFQKNLPd-yAPdFLSSTSaq-------eNYIVcnHLRS 395 Oceanobacillus i...
NP_389223   341 KEDFIQYMIEVSDyLLPFLKNRAVTVIRYPHGsr----seSFFQKNKPd-yAPdFVQSFYdg------shEHIVceDMST 409 Bacillus subtili...
ZP_01723895 357 KDHYLSYLQSVSPyLLPFLQDRPLTVIRYPHGvp----geSFYQKSRPd-kLPnFVATAMmd------eiDYIVcnNLET 425 Bacillus sp. B14905
YP_175097   333 KADYLHYLQAVMPfMLPFLYQRALTVIRFPHGtfa---neRFYQKHIPn-yAPaYVNSAWle------diCYILcnNPET 402 Bacillus clausii...
ZP_01188323  27 KGDLINYYINMYPyLKEYLLNRPLSMKSYPDGin----gkSFYQKDCPd-yAPhWLSTYGifsghrkdiiNWVTinKLSD 101 Halothermothrix ...
CAM03450    379 KRDFVRYHARIGPvILPYLVGRPLNTHRYPDGad----kpGFWHKEVPs-hAPyWLTSWRyeaadpdetqNYVIadSVPA 453 Saccharopolyspor...
Feature 1                   #                 # #                                # ### #        
2FAQ_A      108 LVGAVQMGsIEFHTWNASLanleRPDRFVLDLDPdpALPWKRMLEATQLSLTLLDELGLRAFLKTSGGKGMHLLVPLe-r 186 Pseudomonas aeru...
ZP_01170763 409 FLWLGNQLaFEFHIPFQTIks-kGPSEIVFDLDPpsRDAFTLAIKAAIMIKEVLDHLNLTSFVKTSGNKGIQVYIPLpdn 487 Bacillus sp. NRR...
ZP_01575281 103 LVWLCTQAaLELHTSFNVHekpnHPSSLVFDLDPddDLHFEDVAELAGRIHETLEALGIMDFIKTSGATGLQIFVPVa-a 181 Clostridium cell...
NP_243075   412 LVWLGNQLaLEFHIPYHPVpy-tKPSEIVFDLDPpsISQFSLAVKAAQLMKNMFDALKLQSFVKTSGGKGLQLYLPLpdn 490 Bacillus halodur...
NP_693956   396 IVWLANHGsIEYHIPFQRIgh-vTPLEIVFDLDPpdREHFKLAVHAANLLKHILDELELVSFVKTSGNKGLQVYIPIreg 474 Oceanobacillus i...
NP_389223   410 LLWLCNQLaLEFHVPFQTIks-rRPAEIVIDLDPpsRDDFLMAVQAANELKRLLDSFGITSYPKLSGNKGIQLYIPLspe 488 Bacillus subtili...
ZP_01723895 426 LLWLGNQLaLELHIPFQTRqt-mYPTEIVFDLDPpsTDHFSLAIAGALDLKEIIDYFQLQSFVKTSGGKGLQLYIPLpan 504 Bacillus sp. B14905
YP_175097   403 LIWLGNQLaLELHIPFQTIes-sKPDEIVFDLDPpsQDQFGLAQEAALDMKQIFNRFQLPFFCKTTGGKGLQVHIPLekq 481 Bacillus clausii...
ZP_01188323 102 LVWVANRAsIELHTWFSTTtnldKPDFAVFDLDPgsKSSMKDVVDIALTIKNILDEFNVRSFVKTSGKRGLHVYIPVk-t 180 Halothermothrix ...
CAM03450    454 LAWLANYAaLELHPWTSWAsdveHPTWALFDIDPgsKTSFEDVLALARLHRTALEHLGVRAGPKVTGQRGVQIWVPIa-p 532 Saccharopolyspor...
Feature 1                                                #  #     #       ###              
2FAQ_A      187 RHGWDEVKDFAQAISQHLARLMPERfSAVSGPrNRVGKIFVDYLRNsrGASTVAAYSVRARegLPVSVPVFREEL 261 Pseudomonas aeruginosa
ZP_01170763 488 AYTYDDTRLFTSFIADYLISKEPDLfTTERMKkNRGGRLYVDYIQHaeGKTIVAPYSARGNqyAGIAAPLFWEEV 562 Bacillus sp. NRRL B-1...
ZP_01575281 182 KFDYDTARSLNEFFAQYFAEKLRSTvTIERMKkKREGKIYFDWQQMwtGKSMITAYSARAVksAAVSAPIEWSEL 256 Clostridium celluloly...
NP_243075   491 TFTYDDTRLFSKTVCELLCSQFPEDfTTERLKkHRGQRLYLDYLQHdeGKTIVAPFSPRGNegGFIATPLRWEEV 565 Bacillus halodurans C...
NP_693956   475 SMTYDETFLFTEAIAKTLEKSYPNDfTTERMKkNRHNRLYIDYVQHgkDKTLIAPYSPRMTkeGTVSTPLYWNEV 549 Oceanobacillus iheyen...
NP_389223   489 AFTYEETRQFTQLIAEYCTNAFPELfTTERLIkNRHCKLYLDYLQHaeGKTIICPYSTRGNelGTVAAPLYWHEV 563 Bacillus subtilis sub...
ZP_01723895 505 KFTYEEVRVFTEFVCRFLCQQKPHLyTIERLKkNRHNKLYLDYVQHaeGKTIIAPYSTRGNelGLVATPLHWEEV 579 Bacillus sp. B14905
YP_175097   482 TLTYEETGRFMKFVADFLCQQKPGKyTTERLKkKRRNRLYIDYVQHayNKTVIAPYSMRET--GFAAVPLREDEL 554 Bacillus clausii KSM-K16
ZP_01188323 181 RYTYKEIRSFLQNVAEMVIKLKPEQaTVEWRKnKRQGKVYIDYRQNgkSKTLPAPYSLRPTskATVSTPLKWSEI 255 Halothermothrix oreni...
CAM03450    533 HYTYEETRRWVEKVSKAIGATVPDLvSWAWQKnERRGLARLDYTQNvvNKTLVAPYSARPRpgAPVSVPISWDEL 607 Saccharopolyspora ery...

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