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1vs0

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[[Image:1vs0.gif|left|200px]]
[[Image:1vs0.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1vs0 |SIZE=350|CAPTION= <scene name='initialview01'>1vs0</scene>, resolution 2.400&Aring;
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The line below this paragraph, containing "STRUCTURE_1vs0", creates the "Structure Box" on the page.
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|SITE=
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|LIGAND= <scene name='pdbligand=APK:5&#39;-O-[(S)-{[(5S)-5-AMINO-6-OXOHEXYL]AMINO}(HYDROXY)PHOSPHORYL]ADENOSINE'>APK</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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|GENE= Rv0938, MT0965 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK08224 ligC], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam04679 DNA_ligase_A_C], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01068 DNA_ligase_A_M]</span>
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{{STRUCTURE_1vs0| PDB=1vs0 | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vs0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vs0 OCA], [http://www.ebi.ac.uk/pdbsum/1vs0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1vs0 RCSB]</span>
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'''Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A'''
'''Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A'''
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[[Category: Shuman, S.]]
[[Category: Shuman, S.]]
[[Category: TBSGC, TB Structural Genomics Consortium.]]
[[Category: TBSGC, TB Structural Genomics Consortium.]]
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[[Category: ligase]]
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[[Category: Ligase]]
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[[Category: nucleotidyl transferase]]
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[[Category: Nucleotidyl transferase]]
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[[Category: ob fold]]
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[[Category: Ob fold]]
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[[Category: protein structure initiative]]
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[[Category: Protein structure initiative]]
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[[Category: psi]]
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[[Category: Psi]]
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[[Category: structural genomic]]
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[[Category: Structural genomic]]
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[[Category: tb structural genomics consortium]]
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[[Category: Tb structural genomics consortium]]
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[[Category: tbsgc]]
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[[Category: Tbsgc]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 12:51:19 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:27:53 2008''
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Revision as of 09:51, 3 May 2008

Image:1vs0.gif

Template:STRUCTURE 1vs0

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 Sat May 3 12:51:19 2008

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