1vs0: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[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]] | ||
| Line 26: | Line 35: | ||
[[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
| |||||||||||||
| 1vs0, resolution 2.400Å | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ligands: | ZN, CL and MG | ||||||||||||
| 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
Proteopedia Page Contributors and Editors (what is this?)
- Pages with broken file links
- 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
