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1vs0
From Proteopedia
(New page: 200px<br /><applet load="1vs0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vs0, resolution 2.400Å" /> '''Crystal Structure o...) |
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| - | [[Image:1vs0.gif|left|200px]]<br /><applet load="1vs0" size=" | + | [[Image:1vs0.gif|left|200px]]<br /><applet load="1vs0" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1vs0, resolution 2.400Å" /> | caption="1vs0, resolution 2.400Å" /> | ||
'''Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A'''<br /> | '''Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A'''<br /> | ||
==Overview== | ==Overview== | ||
| - | DNA ligase D (LigD) is a large polyfunctional enzyme involved in | + | 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== | ==About this Structure== | ||
| - | 1VS0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with ZN, CL and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1VS0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VS0 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Akey, D.]] | [[Category: Akey, D.]] | ||
[[Category: Aniukwu, J.]] | [[Category: Aniukwu, J.]] | ||
| - | [[Category: Berger, J | + | [[Category: Berger, J M.]] |
| - | [[Category: Glickman, M | + | [[Category: Glickman, M S.]] |
[[Category: Martins, A.]] | [[Category: Martins, A.]] | ||
[[Category: Shuman, S.]] | [[Category: Shuman, S.]] | ||
| - | [[Category: TBSGC, TB | + | [[Category: TBSGC, TB Structural Genomics Consortium.]] |
[[Category: CL]] | [[Category: CL]] | ||
[[Category: MG]] | [[Category: MG]] | ||
| Line 30: | Line 30: | ||
[[Category: tbsgc]] | [[Category: tbsgc]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:38:01 2008'' |
Revision as of 13:38, 21 February 2008
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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 with , and as ligands. 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 Feb 21 15:38:01 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 genomics | Tb structural genomics consortium | Tbsgc
