1r66
From Proteopedia
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|PDB= 1r66 |SIZE=350|CAPTION= <scene name='initialview01'>1r66</scene>, resolution 1.44Å | |PDB= 1r66 |SIZE=350|CAPTION= <scene name='initialview01'>1r66</scene>, resolution 1.44Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> | + | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TYD:THYMIDINE-5'-+DIPHOSPHATE'>TYD</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46] </span> |
|GENE= DesIV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 Streptomyces venezuelae]) | |GENE= DesIV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 Streptomyces venezuelae]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1r6d|1R6D]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r66 OCA], [http://www.ebi.ac.uk/pdbsum/1r66 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r66 RCSB]</span> | ||
}} | }} | ||
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[[Category: Cleland, W W.]] | [[Category: Cleland, W W.]] | ||
[[Category: Holden, H M.]] | [[Category: Holden, H M.]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: NAD]] | ||
| - | [[Category: TYD]] | ||
[[Category: dehydratase]] | [[Category: dehydratase]] | ||
[[Category: rossmann fold]] | [[Category: rossmann fold]] | ||
[[Category: short-chain dehydrogenase/reductase]] | [[Category: short-chain dehydrogenase/reductase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:23:49 2008'' |
Revision as of 20:23, 30 March 2008
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| , resolution 1.44Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | DesIV (Streptomyces venezuelae) | ||||||
| Activity: | dTDP-glucose 4,6-dehydratase, with EC number 4.2.1.46 | ||||||
| Related: | 1R6D
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound
Overview
Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found in some macrolide antibiotics. In Streptomyces venezuelae, there are seven genes required for the biosynthesis of this unusual sugar. One of the genes, desIV, codes for a dTDP-glucose 4,6-dehydratase, which is referred to as DesIV. The reaction mechanisms for these types of dehydratases are quite complicated with proton abstraction from the sugar 4'-hydroxyl group and hydride transfer to NAD+, proton abstraction at C-5, and elimination of the hydroxyl group at C-6 of the sugar, and finally return of a proton to C-5 and a hydride from NADH to C-6. Here we describe the cloning, overexpression, and purification, and high resolution x-ray crystallographic analysis to 1.44 A of wild-type DesIV complexed with dTDP. Additionally, for this study, a double site-directed mutant protein (D128N/E129Q) was prepared, crystallized as a complex with NAD+ and the substrate dTDP-glucose and its structure determined to 1.35 A resolution. In DesIV, the phenolate group of Tyr(151) and O(gamma) of Thr(127) lie at 2.7 and 2.6 A, respectively from the 4'-hydroxyl group of the dTDP-glucose substrate. The side chain of Asp(128) is in the correct position to function as a general acid for proton donation to the 6'-hydroxyl group while the side chain of Glu(129) is ideally situated to serve as the general base for proton abstraction at C-5. This investigation provides further detailed information for understanding the exquisite chemistry that occurs in these remarkable enzymes.
About this Structure
1R66 is a Single protein structure of sequence from Streptomyces venezuelae. Full crystallographic information is available from OCA.
Reference
High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae., Allard ST, Cleland WW, Holden HM, J Biol Chem. 2004 Jan 16;279(3):2211-20. Epub 2003 Oct 21. PMID:14570895
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