2OWO image
Deposition Date 2007-02-16
Release Date 2007-05-15
Last Version Date 2023-08-30
Entry Detail
PDB ID:
2OWO
Keywords:
LIGASE/DNA
Title:
Last Stop on the Road to Repair: Structure of E.coli DNA Ligase Bound to Nicked DNA-Adenylate
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 83333)
(Taxon ID: )
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.30 Å
R-Value Free:
0.25
R-Value Work:
0.21
Space Group:
C 1 2 1
2OWO validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA ligase
Gene (Uniprot):ligA
Chain IDs:D (auth: A)
Chain Length:671
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P15042 Pfam ID:PF22745, PF01653, PF03120, PF03119, PF14520, PF00633, PF00533 EC:6.5.1.2
Polymer Type:polydeoxyribonucleotide
Molecule:26-MER
Chain IDs:A (auth: B)
Chain Length:26
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3'
Chain IDs:C (auth: D)
Chain Length:13
Number of Molecules:1
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
OMC B C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
Ligand Molecules
AMP
SO4
ZN
Primary Citation
Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate.
Mol.Cell 26 257 271 (2007)
PMID: 17466627 DOI: 10.1016/j.molcel.2007.02.026

Abstact

NAD(+)-dependent DNA ligases (LigA) are ubiquitous in bacteria and essential for growth. Their distinctive substrate specificity and domain organization vis-a-vis human ATP-dependent ligases make them outstanding targets for anti-infective drug discovery. We report here the 2.3 A crystal structure of Escherichia coli LigA bound to an adenylylated nick, which captures LigA in a state poised for strand closure and reveals the basis for nick recognition. LigA envelopes the DNA within a protein clamp. Large protein domain movements and remodeling of the active site orchestrate progression through the three chemical steps of the ligation reaction. The structure inspires a strategy for inhibitor design.

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Primary Citation of related structures
2OWO