1X9N,2HIV,2CFM


Conserved Protein Domain Family
OBF_DNA_ligase

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cd07893: OBF_DNA_ligase 
Click on image for an interactive view with Cn3D
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases.
ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.
Statistics
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PSSM-Id: 153435
View PSSM: cd07893
Aligned: 11 rows
Threshold Bit Score: 170.607
Threshold Setting Gi: 112490160
Created: 2-Oct-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA binding
Conserved site includes 18 residues -Click on image for an interactive view with Cn3D
Feature 1:DNA binding site [nucleic acid binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                              #                      ## ######                          
1X9N_A       524 DTLDLVVIGAYLgrg-kraGRYGGFLLASYDEds-----eELQAICKLGTGFSDEELEEHHQSLKAlvlpsprpy----v 593 human
2HIV_A       464 DTVDLVVVGGFYgkg-krgGKISSLLMAAYNPkt-----dSFESVCKVASGFSDEQLDELQKKLMEikrdvkhp------ 531 Sulfolobus solf...
2CFM_A       426 ENLDLVIIGAEWgeg-rraHLFGSFILGAYDPet-----gEFLEVGKVGSGFTDDDLVEFTKXLKPliik---------- 489 Pyrococcus furi...
NP_001006215 599 DTADLVVLGAFYgkg-skgGMMSIFLMGCYDPts-----eKWCTVTKCAGGHDDATLARLQTELDMvkiskdpskipswl 672 chicken
NP_001025987 465 DELDLLIVGGYWgkg-srgGMMSHFLCAVAETpapnekptVFHSICRVGSGYTMKELYDLGLKLAKhwkpynrkdpp-cn 542 chicken
NP_615688    437 ETFDLVVVGSYYgkg-krkGSFGALLCAVLNEee-----qQFETFTKVGTGFTEADAEEINSLLSAhtvseapkn----v 506 Methanosarcina ...
EET90080     434 DTIDVAIVGYYLgrgsrasFKFGGLLCAVYNKkr-----dMFETISRLGSGFTEKQMSELEELLSKiktqakpa------ 502 uncultured eury...
EAY56804     445 DTLDLVIIGFYRgkgqrtrLGIGAILTAAYDReq-----dKFVSIARIGSGLTEAQWITLREMLEEstlperpp------ 513 Leptospirillum ...
EES52466     456 DTVDLALIGYYRgkglrtkLGIGAVLGAVYDAgr-----gEFQSVARIGSGLTEEGWRDLRGLLEElrtdgppp------ 524 Leptospirillum ...
YP_002250496 427 DTVDCVILGYFKgrghrakFGIGALLVGVYDDer-----dLFKTIAKIGTGPTEEEWVKFREILDEikvekrpn------ 495 Dictyoglomus th...
ZP_03857409  433 DTVDCVIVGYIYgrgkraqLGAGALLVAVYNPdk-----dTFQTITKIGTGLTDEEWKEVVERCKPyvteekpa------ 501 Thermobaculum t...
Feature 1                                    # ## #               #### #                
1X9N_A       594 ridgavipDHWLD---PSAVWEVKCADLSLSPIYPaarglv--dsdkgISLRFPRFIRVR---EDKQPEQA 656 human
2HIV_A       532 rvnskmepDIWVE---PVYVAEIIGSEITISPLHTccqdvv--ekdagLSIRFPRFIRWR---DDKSPEDA 594 Sulfolobus solfataricus
2CFM_A       490 ----eegkRVWLQ---PKVVIEVTYQEIQKSPKYRs-----------gFALRFPRFVALR---DDKGPEDA 539 Pyrococcus furiosus
NP_001006215 673 kinkiyypDFIVPdpkKAPVWEITGAEFSKAEAHTad----------gISIRFPRCTRIR---DDKDWKTA 730 chicken
NP_001025987 543 ilcgtekpEMYIEp-cNSVIVQIKAAEIVNSDMYKt-----------dCTLRFPRIEKIR---EDKEWYEC 598 chicken
NP_615688    507 iikkgmlpDIFIE---PAVVIEVLGSEITNSPGHTagege----eetgLALRFPRFLRIR---YDRAPFDA 567 Methanosarcina acetivora...
EET90080     503 rvdslvkpDFWVY---PKYVVTVRADEITKSPMHTcgrekqedgteagYALRFPRLVGEEairSDKSVEEV 570 uncultured euryarchaeote...
EAY56804     514 svlsdiqpEYWVE---PKFVVRVRADDITRSPQHMcgrre----geegYALRFPRMTGEPr--ADKNPFDA 575 Leptospirillum sp. Group...
EES52466     525 gvvsglvpDFWVR---PELVVSVLADELTRSPTHRagrre---geeegFALRFPRMVSGPr--ADKRAEDA 587 Leptospirillum ferrodiaz...
YP_002250496 496 nvesfiepDVWVE---PKYVVVVQADEITRSPVHTcgrel----dglgYALRFPRVQGFVr--EDKGPYDA 557 Dictyoglomus thermophilu...
ZP_03857409  502 rvesiiqpSVWVE---PAVVIEVLADEITRSPVHTagmng----ekqgYALRFPRLVSFRe--SDKRPEDA 563 Thermobaculum terrenum A...

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