2CFM


Conserved Protein Domain Family
OBF_DNA_ligase_Arch_LigB

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cd07972: OBF_DNA_ligase_Arch_LigB 
Click on image for an interactive view with Cn3D
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases 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. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Pyrococcus furiosus DNA ligase, Mycobacterium tuberculosis LigB, and similar archaeal and bacterial proteins. 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: 153441
View PSSM: cd07972
Aligned: 33 rows
Threshold Bit Score: 169.266
Threshold Setting Gi: 119719344
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:
  • Comment:based on similarity to other members of the family

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                    #####    #                  ## ######                               
2CFM_A       426 ENLDLVIIGAEWGEGRRAHLFGSFILGAYDPet-gEFLEVGKVGSGFTDDDLVEFTKXLKPLIIKe-EGKRVWLQPKVVI 503  Pyrococcus fur...
NP_897414    424 MTLDAVLLYAQAGSGRRANLFTDYTFGLWSDaaepQLVSFAKAYSGLNDEEILELDRWIRRNTLQr-FGPARSVKAELVF 502  Synechococcus ...
YP_001275925 427 YTIDAVLIYAQRGSGKRASLYTDYTFAVWDGd---RLTPFAKAYSGLTDEEIRQVDAFVRRNTLEk-FGPVRTVTPELVF 502  Roseiflexus sp...
YP_007949    404 MVIDAVLMYAQAGSGRRANLFTDYTFGIWNQn---ELIPIAKAYSGLDQGEINKLDRWIRMHTEEk-FGPVRKVKTEQVF 479  Candidatus Pro...
YP_002755673 409 ATLDVVVTGAEFGHGKRAHVLSDYTFAVRDGe---ELKNIGKAYSGLTDAEIAANTKFLKEHTLEd-FGHFRSVEPLLVL 484  Acidobacterium...
ZP_02925026  796 STLDVVVVKAEQGHGKRSHVLSDYTFAVRDEhs-gALKVIGKAYSGLSDGEIEELTEHFTEHTLSq-RGSVRTVTPNIVL 873  Verrucomicrobi...
P95096       383 HTLDLVVLAVEWGSGRRRGKLSNIHLGARDPat-gGFVMVGKTFKGMTDAMLDWQTTRFHEIAVGptDGYVVQLRPEQVV 461  Mycobacterium ...
YP_003203854 380 HTFDLAVIAAEWGYGRRQGWLSNLHLAARDPrt-gELVMLGKTFKGLTDATLTWQTEQFLAREVRr-TKSTVFVEPPLVA 457  Nakamurella mu...
NP_864484    427 HTVDAVLIYAQRGHGKRASLYTDYTFAVWDEd---KLVPFAKAYSGLTDAEIRKVDRFVRDNTSEr-FGPVRSVKPELVM 502  Rhodopirellula...
YP_001736720 409 NSLDLVIVAAERGYGRRHRWYSDYYLAARDPes-gEFLIVGKTFKGLTDEEFEWITQKLEELSIGk-EGKLIRVRPRIVV 486  Candidatus Kor...
Feature 1               # ## #    #### #                     
2CFM_A       504 EVTYQEIQKSPKYRSGFALRFPRFVALRDDKGPEDADTIERIAQ 547  Pyrococcus furiosus
NP_897414    503 EIGFEGIHPSKRHKSGIAVRFPRILRWRRDKPADEADRIQTALS 546  Synechococcus sp. WH 8102
YP_001275925 503 ELAFEGIQRSNRHKSGIAVRFPRILRWRRDKRPADADTLEQVRA 546  Roseiflexus sp. RS-1
YP_007949    480 EIAFEGIQRSNRHKSGIALRFPRIKRWRTDKPYQECDDLETIIK 523  Candidatus Protochlamydia amoebophila UWE25
YP_002755673 485 EVAFNNIQRSERHNSGFALRFPRIVRIRDDKPVEEIDTLARVEE 528  Acidobacterium capsulatum ATCC 51196
ZP_02925026  874 EIAFDSIQASQRHDSGLALRFPRIKAIRRDKGVDEIDTLTYARK 917  Verrucomicrobium spinosum DSM 4136
P95096       462 EVALDGVQRSSRYPGGLALRFARVVRYRADKDPAEADTIDAVRA 505  Mycobacterium tuberculosis
YP_003203854 458 EIAIDGVQASTRYPGGIALRFARVLRYRPDKTPDEVDSLDAVVA 501  Nakamurella multipartita DSM 44233
NP_864484    503 ELAFEGLQRSTRHKSGIATRFPRIVRWRTDKQPADADRLADLIA 546  Rhodopirellula baltica SH 1
YP_001736720 487 EVSFNEIQRSPKYKSGFALRFARITRIRDDKSPEEADTIERVRE 530  Candidatus Korarchaeum cryptofilum OPF8

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