1VS0


Conserved Protein Domain Family
OBF_DNA_ligase_LigD

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cd07971: OBF_DNA_ligase_LigD 
Click on image for an interactive view with Cn3D
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD 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 Mycobacterium tuberculosis LigD and similar bacterial proteins. LigD, or DNA ligase D, catalyzes the end-healing and end-sealing steps during nonhomologous end joining. 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: 153440
View PSSM: cd07971
Aligned: 141 rows
Threshold Bit Score: 83.378
Threshold Setting Gi: 145596479
Created: 27-Aug-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA binding
Conserved site includes 13 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                             #                ## #####  #                               
1VS0_A       191 NTQEVVIGGWRAgeggrssGVGSLLXGIPGPg-GLQFAGRVGTGLS--ERELANLKEXLAPLHTDESpfdvplpardAKG 267 Mycobacterium t...
NP_437156    245 KRDAFPIVAFVEklgaqprRIASLYLGRWEGd-RLVYAGKAQTGYT--LTAAREVRERLNPLIIGKSplsh---pinKPK 318 Sinorhizobium m...
ZP_03635174  200 KDEDFAVCGYIQke----rNVLSLVLGQYQGk-TLVYKGHVTLGVS--EALLKKKLPVTAICPFPETpk-------nHEQ 265 Holdemania fili...
ZP_01156664   30 QIGDFAVAGYTTska--agGLAALAVAEPDGd-VLRYVGKVGTGFD--RATAETLLARLEALRDEGGgae-----glPRD 99  Oceanicola gran...
YP_001113345 200 HSAEWVIAGWEKgeg--hrHLGSLILVGFNQg-KWIYMGKVGTGFG--KDDENKLLRLMEPLEIDESvftp--prgeFRS 272 Desulfotomaculu...
O28549       199 NTLDCVIVGWIEgegerakTFGSLVLAVYEDg-RLKHVGNVGTGFD--SEFLNWFSERLREIEVAKPhfe-----ieTKN 270 Archaeoglobus f...
YP_001211793 200 KEADLVICGYQYgpg--gkNLGCLVLGGYHNg-RLVYQGKVGTGFS--SEEANALLEGLRRLEVAGEtlqv--praeKSR 272 Pelotomaculum t...
YP_430340    205 RAGEFIIAGYEPgag--grLLGSLILAECREg-QLVYRGKVGTGFD--RQEEKKLLVELQQLQPGPPpfke--nipeLRK 277 Moorella thermo...
EEO29772     202 MDDDYIICGYVSna----eYVVSLVLGQYDRsgRIIYKGRVTLGKAseDFALIEKQPKVKSWPFPEKpp------ayVDN 271 Oxalobacter for...
ZP_05348170  201 ADEEFVVTGYIPkg----qRIFSLIIAKYHGd-MLVYKGHVTSGVT--REEISSLEVSMRNPFRMLPv--------gNEE 265 Bryantella form...
Feature 1                             # ## #             
1VS0_A       268 ITYVKPALVAEVRYSEWTPEgRLRQSSWRGLRPDKKPSEV 307 Mycobacterium tuberculosis
NP_437156    319 ATWVEPQVYAEIDYGGVTDDgLLREPVFKGLQDVSRAAGK 358 Sinorhizobium meliloti 1021
ZP_03635174  266 AVWLKPKLVCTVKYMDKTAAgSLRQPVLKGFREDKTAKEC 305 Holdemania filiformis DSM 12042
ZP_01156664  100 VVPVRPLLTAHVHFTARNRTeALRHAVFKGLREVTLARAP 139 Oceanicola granulosus HTCC2516
YP_001113345 273 PVWVKPTLICEVTFTEISPEgRLRHPSYKGLRYDKNPQEC 312 Desulfotomaculum reducens MI-1
O28549       271 VHWVKPRYVCEVEFLEFTEDgKLRAPVFLRLREDKSPDEC 310 Archaeoglobus fulgidus
YP_001211793 273 TRWVRPLLVCAVEYLEATAGgCLRHPVYRGLRRDKTPAEC 312 Pelotomaculum thermopropionicum SI
YP_430340    278 PRWVQPRLVCTVEYLELTPDgRLRHPTYRGLRWDKAPWEC 317 Moorella thermoacetica ATCC 39073
EEO29772     272 ATWIRPKLVCKVAFMARNHNgLMRQPVYRGLRPDKTAKET 311 Oxalobacter formigenes OXCC13
ZP_05348170  266 AIWVVPDHVCVVEYMPNTLN-SLRQPVFKGFRDDVFPEEV 304 Bryantella formatexigens DSM 14469

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