2Q2T image
Deposition Date 2007-05-29
Release Date 2007-07-10
Last Version Date 2024-10-30
Entry Detail
PDB ID:
2Q2T
Keywords:
LIGASE/DNA
Title:
Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick
Biological Source:
Source Organism:
Paramecium bursaria Chlorella virus 1 (Taxon ID: 10506)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.30 Å
R-Value Free:
0.26
R-Value Work:
0.21
Space Group:
P 21 21 21
2Q2T validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chlorella virus DNA ligase
Gene (Uniprot):A544R
Chain IDs:D (auth: A)
Chain Length:319
Number of Molecules:1
Biological Source:Paramecium bursaria Chlorella virus 1
UniProt ID:O41026 Pfam ID:PF01068, PF14743 EC:6.5.1.1
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3'
Chain IDs:A (auth: B)
Chain Length:21
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide/polyribonucleotide hybrid
Molecule:5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'
Chain IDs:B (auth: C)
Chain Length:10
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'
Chain IDs:C (auth: D)
Chain Length:11
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
Primary Citation
Structural basis for nick recognition by a minimal pluripotent DNA ligase.
Nat.Struct.Mol.Biol. 14 770 778 (2007)
PMID: 17618295 DOI: 10.1038/nsmb1266

Abstact

Chlorella virus DNA ligase, the smallest eukaryotic ligase known, has pluripotent biological activity and an intrinsic nick-sensing function, despite having none of the accessory domains found in cellular ligases. A 2.3-A crystal structure of the Chlorella virus ligase-AMP intermediate bound to duplex DNA containing a 3'-OH-5'-PO4 nick reveals a new mode of DNA envelopment, in which a short surface loop emanating from the OB domain forms a beta-hairpin 'latch' that inserts into the DNA major groove flanking the nick. A network of interactions with the 3'-OH and 5'-PO4 termini in the active site illuminates the DNA adenylylation mechanism and the crucial roles of AMP in nick sensing and catalysis. Addition of a divalent cation triggered nick sealing in crystallo, establishing that the nick complex is a bona fide intermediate in the DNA repair pathway.

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Disease

Primary Citation of related structures
1FVI
2Q2U