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1vs0
From Proteopedia
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| - | [[Image:1vs0.gif|left|200px]] | + | [[Image:1vs0.gif|left|200px]] |
| - | + | ||
| - | '''Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A''' | + | {{Structure |
| + | |PDB= 1vs0 |SIZE=350|CAPTION= <scene name='initialview01'>1vs0</scene>, resolution 2.400Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= Rv0938, MT0965 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1VS0 is a [ | + | 1VS0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VS0 OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D., Akey D, Martins A, Aniukwu J, Glickman MS, Shuman S, Berger JM, J Biol Chem. 2006 May 12;281(19):13412-23. Epub 2006 Feb 13. PMID:[http:// | + | Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D., Akey D, Martins A, Aniukwu J, Glickman MS, Shuman S, Berger JM, J Biol Chem. 2006 May 12;281(19):13412-23. Epub 2006 Feb 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16476729 16476729] |
[[Category: Mycobacterium tuberculosis]] | [[Category: Mycobacterium tuberculosis]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: protein structure initiative]] | [[Category: protein structure initiative]] | ||
[[Category: psi]] | [[Category: psi]] | ||
| - | [[Category: structural | + | [[Category: structural genomic]] |
[[Category: tb structural genomics consortium]] | [[Category: tb structural genomics consortium]] | ||
[[Category: tbsgc]] | [[Category: tbsgc]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:48:57 2008'' |
Revision as of 12:48, 20 March 2008
| |||||||
| , resolution 2.400Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Gene: | Rv0938, MT0965 (Mycobacterium tuberculosis) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A
Overview
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.
About this Structure
1VS0 is a Single protein structure of sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA.
Reference
Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D., Akey D, Martins A, Aniukwu J, Glickman MS, Shuman S, Berger JM, J Biol Chem. 2006 May 12;281(19):13412-23. Epub 2006 Feb 13. PMID:16476729
Page seeded by OCA on Thu Mar 20 14:48:57 2008
Categories: Mycobacterium tuberculosis | Single protein | Akey, D. | Aniukwu, J. | Berger, J M. | Glickman, M S. | Martins, A. | Shuman, S. | TBSGC, TB Structural Genomics Consortium. | CL | MG | ZN | Ligase; ob fold; nucleotidyl transferase | Protein structure initiative | Psi | Structural genomic | Tb structural genomics consortium | Tbsgc
