1X9N,2HIV


Conserved Protein Domain Family
OBF_DNA_ligase_I

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cd07969: OBF_DNA_ligase_I 
Click on image for an interactive view with Cn3D
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit.
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 ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). 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: 153438
View PSSM: cd07969
Aligned: 60 rows
Threshold Bit Score: 188.069
Threshold Setting Gi: 253744801
Created: 27-Aug-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA binding
Conserved site includes 23 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       523 GDTLDLVVIGAYLGRGKRA-GRYGGFLLASYDEdsEELQAICKLGTGFSDEELEEHHQSLKALVLpspRPYVRIDgaVIP 601 human
Q9HJ26       434 WDTLDLTVVGAFYGHGRRK-GTYGALLLATYNDknDTFETVCKLGSGFSDDVLFSLPKKFEQYVSkekPARVISN--LEP 510 Thermoplasma ac...
O67398       432 ADTLDLVVVGGFYGKGQRK-GTFGSLLMACYDPesDMFKTVTKVGTGFTEDDFKKLEEILMPRKLnhrHPRVNSI--LEA 508 Aquifex aeolicus
A0RWD6       433 GDSLDLVIIGAFFGKGRRT-GRYGTLLLATYDDsrDTFPSICKVGTGFTDEDLDQLYQLLSPRVTlkrNPRIDSG--MEA 509 Cenarchaeum sym...
AAK96101     434 GDSLDLVVIGGFFGKGRRT-GSYGTLLLATYDQntDTFPSICKVGTGFTDESLDQLYQILNPKITikkNPRVNSE--MEA 510 uncultured cren...
YP_001736814 435 IEPVDLVVVGAFWGKGKRA-GTYGALLMAAYSPeeDVFKTVCKMGSGFTDEELARMPKLLEDYKIdhkHPSVISN--IEA 511 Candidatus Kora...
NP_615688    436 RETFDLVVVGSYYGKGKRK-GSFGALLCAVLNEeeQQFETFTKVGTGFTEADAEEINSLLSAHTVseaPKNVIIKkgMLP 514 Methanosarcina ...
EET90080     433 SDTIDVAIVGYYLGRGSRAsFKFGGLLCAVYNKkrDMFETISRLGSGFTEKQMSELEELLSKIKTqakPARVDSL--VKP 510 uncultured eury...
EAY56804     444 SDTLDLVIIGFYRGKGQRTrLGIGAILTAAYDReqDKFVSIARIGSGLTEAQWITLREMLEESTLperPPSVLSD--IQP 521 Leptospirillum ...
YP_002250496 426 ADTVDCVILGYFKGRGHRAkFGIGALLVGVYDDerDLFKTIAKIGTGPTEEEWVKFREILDEIKVekrPNNVESF--IEP 503 Dictyoglomus th...
Feature 1                         # ## #               #### #                            
1X9N_A       602 DHWLDPSAVWEVKCADLSLSPIYPAARGlv--dsDKGISLRFPRFIRVR---EDKQPEQATTSAQVACLYRK 668 human
Q9HJ26       511 DVWFYPAVVMEVIGAEITVSPIHTCAYGei--ekDSGLSVRFPRFTGKWr--EDKKPEDSTTSREILEMYKE 578 Thermoplasma acidophilum
O67398       509 DMWFEPYLVLEITGAELTLSPVHTCGWGkv--spNRGIGLRFPRFTGRYr--FDKRPEDATTEQEIIEMYRM 576 Aquifex aeolicus
A0RWD6       510 DVWFDPEVVMEVVASEITLSPVHKTALDsv--rkGAGLALRFPKFTGKLr--TEKTAEDASTDQEVIALYKS 577 Cenarchaeum symbiosum
AAK96101     511 DVWFEPELVIEVVASEITLSPIHKTAIXei--rkDTGLALRFPKFTGKIr--VEKTVEDASTDEEVMSLYKG 578 uncultured crenarchaeot...
YP_001736814 512 DVYFVPVKVAQVLGDEITLSPTHTCGWNkv--rkNAGLAIRFPRFMGWR---DDKGPQDATTEEEIIEMYKE 578 Candidatus Korarchaeum ...
NP_615688    515 DIFIEPAVVIEVLGSEITNSPGHTAGEGe----eETGLALRFPRFLRIR---YDRAPFDATTVREIRDLKEG 579 Methanosarcina acetivor...
EET90080     511 DFWVYPKYVVTVRADEITKSPMHTCGREkqedgtEAGYALRFPRLVGEEairSDKSVEEVNQTSEIIEMYKM 582 uncultured euryarchaeot...
EAY56804     522 EYWVEPKFVVRVRADDITRSPQHMCGRRe----gEEGYALRFPRMTGEPr--ADKNPFDATTVLEIKNLYQK 587 Leptospirillum sp. Grou...
YP_002250496 504 DVWVEPKYVVVVQADEITRSPVHTCGREl----dGLGYALRFPRVQGFVr--EDKGPYDATTVKEILEMFRN 569 Dictyoglomus thermophil...

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