1VS0

Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A

Summary for 1VS0

• Entry DOI: 10.2210/pdb1vs0/pdb
• Descriptor: Putative DNA ligase-like protein Rv0938/MT0965, ZINC ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: ligase; ob fold; nucleotidyl transferase, structural genomics, psi, protein structure initiative, tb structural genomics consortium, tbsgc, ligase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 2
• Total formula weight: 69898.51

Authors

Akey, D.,Martins, A.,Aniukwu, J.,Glickman, M.S.,Shuman, S.,Berger, J.M.,TB Structural Genomics Consortium (TBSGC) (deposition date: 2006-01-27, release date: 2006-02-28, Last modification date: 2011-07-13)

Primary citation

Akey, D.,Martins, A.,Aniukwu, J.,Glickman, M.S.,Shuman, S.,Berger, J.M.
Crystal Structure and Nonhomologous End-joining Function of the Ligase Component of Mycobacterium DNA Ligase D.
J.Biol.Chem., 281:13412-13423, 2006

PubMed Abstract: DNA ligase D (LigD) is a large polyfunctional enzyme involved in nonhomologous end-joining (NHEJ) in mycobacteria. LigD consists of a C-terminal ATP-dependent ligase domain fused to upstream polymerase and phosphoesterase modules. Here we report the 2.4 angstroms crystal structure of the ligase domain of Mycobacterium LigD, captured as the covalent ligase-AMP intermediate with a divalent metal in the active site. A chloride anion on the protein surface coordinated by the ribose 3'-OH and caged by arginine and lysine side chains is a putative mimetic of the 5'-phosphate at a DNA nick. Structure-guided mutational analysis revealed distinct requirements for the adenylylation and end-sealing reactions catalyzed by LigD. We found that a mutation of Mycobacterium LigD that ablates only ligase activity results in decreased fidelity of NHEJ in vivo and a strong bias of mutagenic events toward deletions instead of insertions at the sealed DNA ends. This phenotype contrasts with the increased fidelity of double-strand break repair in deltaligD cells or in a strain in which only the polymerase function of LigD is defective. We surmise that the signature error-prone quality of bacterial NHEJ in vivo arises from a dynamic balance between the end-remodeling and end-sealing steps.

PubMed: 16476729
DOI: 10.1074/jbc.M513550200

Experimental method

X-RAY DIFFRACTION (2.4 Å)