2Q2U,1FVI


Conserved Protein Domain Family
OBF_kDNA_ligase_like

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cd08041: OBF_kDNA_ligase_like 
Click on image for an interactive view with Cn3D
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like 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. The mitochondrial DNA of parasitic protozoan is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and oligonucleotide/oligosaccharide binding (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: 153443
View PSSM: cd08041
Aligned: 61 rows
Threshold Bit Score: 62.1509
Threshold Setting Gi: 196229305
Created: 10-Nov-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA binding
Conserved site includes 15 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                   #                              ##             ## ######             
2Q2U_A      212 KDAEATIISMTALfkntntktkdnfgyskrsthksgkveEDVMGSIEVDYD----GVVFSIGTGFDADQRRDFWQnke-- 285 Paramecium bursa...
ZP_03128170 182 EDAEAVVLDTYEGmsnlneaqrdafgrtkrssaqagkvgRGELGGFIVKLVd--sDVEFRLGYNHVLGGVDRVTLwhqre 259 Chthoniobacter f...
YP_189099   341 HTVDLRCLRVEEHv------------------------rGNKVGNIVVDYK----GYELGVGSGFSDKDRKLFWEqkd-- 390 Staphylococcus e...
ZP_05399404 334 NTCDIKCIDIEEGdg----------------------kyKDLLGSIICDYK----GYRLGVGSGFTDEQRKYYFInqn-- 385 Clostridium diff...
CBH12070    423 HDAEYRIVDFLPGng----------------------kfEGGLGAFVCETSt---GIRFNATPKTTTKRRLELWAerd-- 475 Trypanosoma bruc...
CBH12071    392 QDSEYIIVDGVEGrg----------------------kwRGCLGAFVCQTRa---GHRFTVAPATTEERKREMWHrln-- 444 Trypanosoma bruc...
NP_893796   346 IEVTLRVVAIEEGtg----------------------rnEGRLGAILVEGKddqyNYRLNCGSGFSDSQREEYWSkkd-- 401 Prochlorococcus ...
XP_757337   601 KDAEYTVQAITVTtmrlpi--------------ggrfqeHKAMASIQIEHK----GTRVSVGSGFTPDQRVEFANdpd-- 660 Ustilago maydis 521
XP_570707   574 QDAEYVVKSADTNimrlai--------------ngvfdeHEALASVWIEHK----GHPVSVGSGFSAEERLRYAEkpe-- 633 Cryptococcus neo...
ZP_02468155 220 VTFDLRIVGVEEGeg----------------------kyEGTAGKIVLQFAd---GTPVKAAGGTNAEREQWFFNpt--- 271 Burkholderia tha...
Feature 1                #                                   #  # #     
2Q2U_A      286 syIGKMVKFKYFEMgs---------------------------kdCPRFPVFIGIR 314 Paramecium bursaria Chlorella virus 1
ZP_03128170 260 slIGRLVKFKHQPSga---------------------------keAPRFPKFVGFR 288 Chthoniobacter flavus Ellin428
YP_189099   391 liEGKIVEISYFEEsknd-----------------------kggeSLRFPVFKMVR 423 Staphylococcus epidermidis RP62A
ZP_05399404 386 kiLGRVIEVKFFEEtnne-----------------------kgelSLRFPVFLRVR 418 Clostridium difficile QCD-37x79
CBH12070    476 rlLGKYLTVQYQELss---------------------------qdVPRFPIAKCVR 504 Trypanosoma brucei gambiense DAL972
CBH12071    445 vyKGKMLTVQYQELst---------------------------ngVPRFPIGKCVR 473 Trypanosoma brucei gambiense DAL972
NP_893796   402 klIGQLVEIRADARtqsqd----------------------aetfSLRFPRFKCFR 435 Prochlorococcus marinus subsp. pastoris ...
XP_757337   661 kiVGKIVTVEYFDEskttvgtsgsaeplqsedgqgekadsrkqvySLRFPRLKQIW 716 Ustilago maydis 521
XP_570707   634 eiVGKTITVEYFSEseaig---------------------regakSLRFPRVKAIW 668 Cryptococcus neoformans var. neoformans ...
ZP_02468155 272 aiIGKIGEVACLERlp---------------------------sgELREPVFKGVR 300 Burkholderia thailandensis MSMB43

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