1vs0: Difference between revisions
New page: left|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]] | ||
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[[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 ZN, CL and MG 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
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 genomics
- Tb structural genomics consortium
- Tbsgc
