Conserved Protein Domain Family
OBF_DNA_ligase_III

?
cd07967: OBF_DNA_ligase_III 
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III 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). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/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
?
PSSM-Id: 153436
View PSSM: cd07967
Aligned: 14 rows
Threshold Bit Score: 220.697
Threshold Setting Gi: 66810247
Created: 27-Aug-2009
Updated: 2-Oct-2020
Structure
?
Aligned Rows:
 
DNA binding
Feature 1:DNA binding site [nucleic acid binding site]
Evidence:
  • Comment:based on similarity to other members of the family

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                       #####    #                 ## ######                              
NP_001006215  597 MADTADLVVLGAFYGKGSKGGMMSIFLMGCYDPTsEKWCTVTKCAGGHDDATLARLQTELDMv--KISKDPSKIPSWLK- 673  chicken
XP_001896024  392 MADTADLILLGAFYGXGNKGGTMSVFLMGVYDKEkQKFCTVTKCGNGHDDATLERINKELEPkmnKISRKYENLPEWIE- 470  agent of lymp...
Q9VG84        460 MADTADLVVLGAWYGSGKKGGTLSIFLMGCYDAFgRLWKTVTKVHSGLDDATNAEVHKSLIKl--TERADANAIPSWLL- 536  fruit fly
XP_001745548  643 MADTADLALLGAWFGTGSKGGLLSVYLMGCRDDN-GVWRTVTKCGNGFDDAQVDAYHRKMLPlmqKVSQDRSKVPGWLRi 721  Monosiga brev...
XP_002113418  558 MADSADLVVLGAYYGTGNKGGVMSVFLMGTYDERsGRWRTVAKCGNGHDDKTLDKINKELSVv--KISKDFSKVPGWLN- 634  Trichoplax ad...
XP_786357     602 MADSADLLVLGAFYGTGTKGGMMSVFLMGVYDPNsDSFRTVTKCGNGLDDNTMDKVNRDLDMv--KISKDSSKVPSWLR- 678  purple urchin
XP_001630058  636 MADTADLVVLGAYYGTGNKGGLMSVFLMGVFNPRiKKWCTVAKCGNGHDDKTLDKLNRELKVk--KISKDPNRVPVWLE- 712  starlet sea a...
XP_002129234  577 MADTADLVVLGAYYGTGSKGGMMSVFLMGVYDEKrERWCTVTKVGNGHDDETLEKINKQLKVe--KISKDMKRVPKWLN- 653  Ciona intesti...
EEC10327      574 MADSADLAVLGAYFGTGNKGGIMSIFLMGCWNPAtGRWCTVTKVHGGHDDTTLERLQTELEMt--KISKQADRVPRWLD- 650  black-legged ...
BAH72329        1 MADSADLVVLGAWFGTGNKGGMMSIFLMGCYNEAkKKWCTVTKVHGGHDDKTLERLQGELKMi--KISKDPEKVPEWLK- 77   pea aphid
Feature 1                                    # ## #     #### #                  
NP_001006215  674 INKIYYPDFIVPDPKKAPVWEITGAEFSKAEAHTaDGISIRFPRCTRIRDDKDWKTATNLPQ 735  chicken
XP_001896024  471 CSRSLVPDFIVMDPKESPVWEIAGAEFTRSDNHTaSGISIRFPRVTKIRDDKNWETATSLQE 532  agent of lymphatic filariasis
Q9VG84        537 CSKSLVPDVLAKDPMKMPVWEITGAEFTKSDAHTaSGISVRFPRITRRRSDKSAKEANDLAH 598  fruit fly
XP_001745548  722 DESRLVPDYIIRDPNQAPILEIAGAEFSESRAHSaDGISIRFPRIARVRSDKNADTATSLSE 783  Monosiga brevicollis MX1
XP_002113418  635 VHRSLVPDFIVTDPKTAPVWEITGAEFSQSTVHTaDGISIRFPRVTRIRDDKDWTNATNLDR 696  Trichoplax adhaerens
XP_786357     679 VNKTLVPDFVIREPKKAPVWEIIGAEFTQSETHTaGGISIRFPRVTRIRDDKDFETATDLPR 740  purple urchin
XP_001630058  713 VHRSLIPDFVVDDPKKAPVWEITGAEFSKSTTHTaDGISIRFPRVTRIRDDKDWETATDLDL 774  starlet sea anemone
XP_002129234  654 LNKNHVPDLVVADPKNAPVWEITGTEFTQSESHTaEGISIRFPRVTKIRRDKNWKTATSLER 715  Ciona intestinalis
EEC10327      651 VQKPLVPDFVAKDPNNTQVWEISGAEFTRAEIHTaDGISIRFPRVTRIRYDKTPKEATSLPE 712  black-legged tick
BAH72329       78 CTKTMIPDFVAEDPKKMPVWEISGAEFSQAEVHTaNGISIRFPRVTKIRNDKDWKTATSLTE 139  pea aphid

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap