1r66
From Proteopedia
(New page: 200px<br /><applet load="1r66" size="450" color="white" frame="true" align="right" spinBox="true" caption="1r66, resolution 1.44Å" /> '''Crystal Structure of...) |
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| - | [[Image:1r66.jpg|left|200px]]<br /><applet load="1r66" size=" | + | [[Image:1r66.jpg|left|200px]]<br /><applet load="1r66" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1r66, resolution 1.44Å" /> | caption="1r66, resolution 1.44Å" /> | ||
'''Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound'''<br /> | '''Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found in some | + | 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== | ==About this Structure== | ||
| - | 1R66 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae] with CL, NAD and TYD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http:// | + | 1R66 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=NAD:'>NAD</scene> and <scene name='pdbligand=TYD:'>TYD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R66 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Streptomyces venezuelae]] | [[Category: Streptomyces venezuelae]] | ||
[[Category: dTDP-glucose 4,6-dehydratase]] | [[Category: dTDP-glucose 4,6-dehydratase]] | ||
| - | [[Category: Allard, S | + | [[Category: Allard, S T.M.]] |
| - | [[Category: Cleland, W | + | [[Category: Cleland, W W.]] |
| - | [[Category: Holden, H | + | [[Category: Holden, H M.]] |
[[Category: CL]] | [[Category: CL]] | ||
[[Category: NAD]] | [[Category: NAD]] | ||
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[[Category: short-chain dehydrogenase/reductase]] | [[Category: short-chain dehydrogenase/reductase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:47:28 2008'' |
Revision as of 12:47, 21 February 2008
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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 with , and as ligands. Active as dTDP-glucose 4,6-dehydratase, with EC number 4.2.1.46 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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