2uzh: Difference between revisions
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'''MYCOBACTERIUM SMEGMATIS 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE (ISPF)''' | {{Structure | ||
|PDB= 2uzh |SIZE=350|CAPTION= <scene name='initialview01'>2uzh</scene>, resolution 2.20Å | |||
|SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Cdf+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Chain+B'>AC3</scene>, <scene name='pdbsite=AC4:Cdf+Binding+Site+For+Chain+B'>AC4</scene>, <scene name='pdbsite=AC5:Zn+Binding+Site+For+Chain+C'>AC5</scene>, <scene name='pdbsite=AC6:Cdf+Binding+Site+For+Chain+C'>AC6</scene>, <scene name='pdbsite=AC7:Edo+Binding+Site+For+Chain+C'>AC7</scene>, <scene name='pdbsite=AC8:Edo+Binding+Site+For+Chain+A'>AC8</scene>, <scene name='pdbsite=AC9:Ipe+Binding+Site+For+Chain+B'>AC9</scene>, <scene name='pdbsite=BC1:Gol+Binding+Site+For+Chain+C'>BC1</scene>, <scene name='pdbsite=BC2:Gol+Binding+Site+For+Chain+A'>BC2</scene>, <scene name='pdbsite=BC3:Gol+Binding+Site+For+Chain+B'>BC3</scene>, <scene name='pdbsite=BC4:Act+Binding+Site+For+Chain+C'>BC4</scene>, <scene name='pdbsite=BC5:Peg+Binding+Site+For+Chain+B'>BC5</scene> and <scene name='pdbsite=BC6:Peg+Binding+Site+For+Chain+B'>BC6</scene> | |||
|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CDF:CYTIDINE-5'-DIPHOSPHATE'>CDF</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> and <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] | |||
|GENE= | |||
}} | |||
'''MYCOBACTERIUM SMEGMATIS 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE (ISPF)''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2UZH is a [ | 2UZH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UZH OCA]. | ||
==Reference== | ==Reference== | ||
The structure of Mycobacteria 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery., Buetow L, Brown AC, Parish T, Hunter WN, BMC Struct Biol. 2007 Oct 23;7:68. PMID:[http:// | The structure of Mycobacteria 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery., Buetow L, Brown AC, Parish T, Hunter WN, BMC Struct Biol. 2007 Oct 23;7:68. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17956607 17956607] | ||
[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]] | [[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]] | ||
[[Category: Mycobacterium smegmatis]] | [[Category: Mycobacterium smegmatis]] | ||
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[[Category: non-mevalonate pathway of isoprenoid biosynthesis]] | [[Category: non-mevalonate pathway of isoprenoid biosynthesis]] | ||
''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 18:41:35 2008'' | ||
Revision as of 19:41, 20 March 2008
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| , resolution 2.20Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , , , , , , and | ||||||
| Ligands: | , , , , , and | ||||||
| Activity: | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, with EC number 4.6.1.12 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
MYCOBACTERIUM SMEGMATIS 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE (ISPF)
OverviewOverview
BACKGROUND: The prevalence of tuberculosis, the prolonged and expensive treatment that this disease requires and an increase in drug resistance indicate an urgent need for new treatments. The 1-deoxy-D-xylulose 5-phosphate pathway of isoprenoid precursor biosynthesis is an attractive chemotherapeutic target because it occurs in many pathogens, including Mycobacterium tuberculosis, and is absent from humans. To underpin future drug development it is important to assess which enzymes in this biosynthetic pathway are essential in the actual pathogens and to characterize them. RESULTS: The fifth enzyme of this pathway, encoded by ispF, is 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF). A two-step recombination strategy was used to construct ispF deletion mutants in M. tuberculosis but only wild-type double crossover strains were isolated. The chromosomal copy could be deleted when a second functional copy was provided on an integrating plasmid, demonstrating that ispF is an essential gene under the conditions tested thereby confirming its potential as a drug target. We attempted structure determination of the M. tuberculosis enzyme (MtIspF), but failed to obtain crystals. We instead analyzed the orthologue M. smegmatis IspF (MsIspF), sharing 73% amino acid sequence identity, at 2.2 A resolution. The high level of sequence conservation is particularly pronounced in and around the active site. MsIspF is a trimer with a hydrophobic cavity at its center that contains density consistent with diphosphate-containing isoprenoids. The active site, created by two subunits, comprises a rigid CDP-Zn2+ binding pocket with a flexible loop to position the 2C-methyl-D-erythritol moiety of substrate. Sequence-structure comparisons indicate that the active site and interactions with ligands are highly conserved. CONCLUSION: Our study genetically validates MtIspF as a therapeutic target and provides a model system for structure-based ligand design.
About this StructureAbout this Structure
2UZH is a Single protein structure of sequence from Mycobacterium smegmatis. Full crystallographic information is available from OCA.
ReferenceReference
The structure of Mycobacteria 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery., Buetow L, Brown AC, Parish T, Hunter WN, BMC Struct Biol. 2007 Oct 23;7:68. PMID:17956607
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