2r0t
From Proteopedia
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|PDB= 2r0t |SIZE=350|CAPTION= <scene name='initialview01'>2r0t</scene>, resolution 1.9Å | |PDB= 2r0t |SIZE=350|CAPTION= <scene name='initialview01'>2r0t</scene>, resolution 1.9Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=PGU:N-({3- | + | |LIGAND= <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= wbdK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= wbdK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2gms|2GMS]], [[2gmu|2GMU]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r0t OCA], [http://www.ebi.ac.uk/pdbsum/2r0t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2r0t RCSB]</span> | ||
}} | }} | ||
| Line 24: | Line 27: | ||
[[Category: Cook, P D.]] | [[Category: Cook, P D.]] | ||
[[Category: Holden, H M.]] | [[Category: Holden, H M.]] | ||
| - | [[Category: PGU]] | ||
[[Category: aspartate aminotransferase]] | [[Category: aspartate aminotransferase]] | ||
[[Category: colitose]] | [[Category: colitose]] | ||
| Line 31: | Line 33: | ||
[[Category: x-ray strucutre]] | [[Category: x-ray strucutre]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:55:21 2008'' |
Revision as of 01:55, 31 March 2008
| |||||||
| , resolution 1.9Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | wbdK (Escherichia coli) | ||||||
| Related: | 2GMS, 2GMU
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal sructure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine
Overview
Di- and trideoxysugars are an important class of carbohydrates synthesized by certain plants, fungi, and bacteria. Colitose, for example, is a 3,6-dideoxysugar found in the O-antigens of Gram-negative bacteria such as Escherichia coli, Salmonella enterica, Yersinia pseudotuberculosis, and Vibrio cholerae, among others. These types of dideoxysugars are thought to serve as antigenic determinants and to play key roles in bacterial defense and survival. Four enzymes are required for the biochemical synthesis of colitose starting from mannose-1-phosphate. The focus of this investigation, GDP-4-keto-6-deoxy-d-mannose-3-dehydratase (ColD), catalyzes the third step in the pathway, namely the PLP-dependent removal of the C3'-hydroxyl group from GDP-4-keto-6-deoxymannose. Whereas most PLP-dependent enzymes contain an active site lysine, ColD utilizes a histidine as its catalytic acid/base. The ping-pong mechanism of the enzyme first involves the conversion of PLP to PMP followed by the dehydration step. Here we present the three-dimensional structure of a site-directed mutant form of ColD whereby the active site histidine has been replaced with a lysine. The electron density reveals that the geminal diamine, a tetrahedral intermediate in the formation of PMP from PLP, has been trapped within the active site region. Functional assays further demonstrate that this mutant form of ColD cannot catalyze the dehydration reaction.
About this Structure
2R0T is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation., Cook PD, Holden HM, Biochemistry. 2007 Dec 11;46(49):14215-24. Epub 2007 Nov 13. PMID:17997582
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