Conserved Protein Domain Family

cd08040: OBF_DNA_ligase_family 
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.
PSSM-Id: 153442
View PSSM: cd08040
Aligned: 4 rows
Threshold Bit Score: 103.488
Threshold Setting Gi: 152149440
Created: 10-Nov-2009
Updated: 2-Oct-2020
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]

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
Feature 1                                                #                 ## ######          
1X9N_A    524 DTLDLVVIGAYLgrgk----------------------ragRYGGFLLASYdedseelqaICKLGTGFSDEELEEHHQsl 581 human
2Q2U_A    212 KDAEATIISMTAlfkntntktkdnfgyskrsthksgkveedVMGSIEVDYDg-------vVFSIGTGFDADQRRDFWQnk 284 Paramecium bursari...
1VS0_A    191 NTQEVVIGGWRAgegg----------------------rssGVGSLLXGIPgpgg--lqfAGRVGTGLSERELANLKExl 246 Mycobacterium tube...
O69698    204 RTADCVVAGYRVhks-----------------------gsdAIGSLLLGLYqedg--qlaSVGVIGAFPMAERRRLLTel 258 Mycobacterium tube...
Feature 1                                                                                # ## 
1X9N_A    582 kalvlpsprpyv-------------------ridgavipdhwldPSAVWEVKCADLslspiypaarglvdsdkgiSLRFP 642 human
2Q2U_A    285 e-----------------------------------------syIGKMVKFKYFEMgs---------------kdCPRFP 308 Paramecium bursari...
1VS0_A    247 aplhtdespfdv------------------plpardakgityvkPALVAEVRYSEWtp---------------egRLRQS 293 Mycobacterium tube...
O69698    259 qplvtsfddhpwnwaahvagqrtprknefsrwnvgkdlsfvplrPERVVEVRYDRMeg---------------arFRHTA 323 Mycobacterium tube...
Feature 1     #     
1X9N_A    643 RFIRVR 648 human
2Q2U_A    309 VFIGIR 314 Paramecium bursaria Chlorella virus 1
1VS0_A    294 SWRGLR 299 Mycobacterium tuberculosis
O69698    324 QFNRWR 329 Mycobacterium tuberculosis

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