ISDA: 3VNN

Deposition Date 2012-01-17

Release Date 2012-06-20

Last Version Date 2024-03-20

Entry Detail

PDB ID:

3VNN

Keywords:

LIGASE

Title:

Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.90 Å

R-Value Free:

0.30

R-Value Work:

0.27

R-Value Observed:

0.27

Space Group:

P 41 2 2

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA ligase 4
Gene (Uniprot):LIG4
Chain IDs:A
Chain Length:139
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P49917 Pfam ID:PF01068 EC:6.5.1.1

Primary Citation

Structural insights into the role of domain flexibility in human DNA ligase IV

Ochi, T, Wu, Q, Chirgadze, D.Y, Grossmann, J.G, Bolanos-Garcia, V.M, Blundell, T.L.Show

Structure 20 1212 1222 (2012)

PMID: 22658747 DOI: 10.1016/j.str.2012.04.012

Abstact

Knowledge of the architecture of DNA ligase IV (LigIV) and interactions with XRCC4 and XLF-Cernunnos is necessary for understanding its role in the ligation of double-strand breaks during nonhomologous end joining. Here we report the structure of a subdomain of the nucleotidyltrasferase domain of human LigIV and provide insights into the residues associated with LIG4 syndrome. We use this structural information together with the known structures of the BRCT/XRCC4 complex and those of LigIV orthologs to interpret small-angle X-ray scattering of LigIV in complex with XRCC4 and size exclusion chromatography of LigIV, XRCC4, and XLF-Cernunnos. Our results suggest that the flexibility of the catalytic region is limited in a manner that affects the formation of the LigIV/XRCC4/XLF-Cernunnos complex.

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