1wvg
From Proteopedia
(New page: 200px<br /><applet load="1wvg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wvg, resolution 1.8Å" /> '''Structure of CDP-D-gl...) |
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| - | [[Image:1wvg.gif|left|200px]]<br /><applet load="1wvg" size=" | + | [[Image:1wvg.gif|left|200px]]<br /><applet load="1wvg" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1wvg, resolution 1.8Å" /> | caption="1wvg, resolution 1.8Å" /> | ||
'''Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi'''<br /> | '''Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Tyvelose is a unique 3,6-dideoxyhexose found in the O antigens of some | + | Tyvelose is a unique 3,6-dideoxyhexose found in the O antigens of some pathogenic species of Yersinia and Salmonella. It is produced via a complex biochemical pathway that employs CDP-D-glucose as the starting ligand. CDP-D-glucose 4,6-dehydratase catalyzes the first irreversible step in the synthesis of this 3,6-dideoxysugar by converting CDP-D-glucose to CDP-4-keto-6-deoxyglucose via an NAD+ -dependent intramolecular oxidation-reduction reaction. Here, the cloning, protein purification and X-ray crystallographic analysis of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with the substrate analog CDP-D-xylose are described. Each subunit of the tetrameric enzyme folds into two domains. The N-terminal region contains a Rossmann fold and provides the platform for NAD(H) binding. The C-terminal motif is primarily composed of alpha-helices and houses the binding pocket for the CDP portion of the CDP-D-xylose ligand. The xylose moiety extends into the active-site cleft that is located between the two domains. Key residues involved in anchoring the sugar group to the protein include Ser134, Tyr159, Asn197 and Arg208. Strikingly, Ser134 O gamma and Tyr159 O eta sit within 2.9 A of the 4'-hydroxyl group of xylose. Additionally, the side chains of Asp135 and Lys136 are located at 3.5 and 3.2 A, respectively, from C-5 of xylose. In the structurally related dTDP-D-glucose 4,6-dehydratase, the Asp/Lys pair is replaced with an Asp/Glu couple. On the basis of this investigation, it can be speculated that Tyr159 serves as the catalytic base to abstract the 4'-hydroxyl proton from the sugar and that Asp135 and Lys136 play critical roles in the subsequent dehydration step that leads to the final product. |
==About this Structure== | ==About this Structure== | ||
| - | 1WVG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhi Salmonella enterica subsp. enterica serovar typhi] with APR and CXY as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/CDP-glucose_4,6-dehydratase CDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.45 4.2.1.45] Full crystallographic information is available from [http:// | + | 1WVG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhi Salmonella enterica subsp. enterica serovar typhi] with <scene name='pdbligand=APR:'>APR</scene> and <scene name='pdbligand=CXY:'>CXY</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/CDP-glucose_4,6-dehydratase CDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.45 4.2.1.45] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WVG OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Salmonella enterica subsp. enterica serovar typhi]] | [[Category: Salmonella enterica subsp. enterica serovar typhi]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Holden, H | + | [[Category: Holden, H M.]] |
| - | [[Category: Koropatkin, N | + | [[Category: Koropatkin, N M.]] |
[[Category: APR]] | [[Category: APR]] | ||
[[Category: CXY]] | [[Category: CXY]] | ||
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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 15:48:29 2008'' |
Revision as of 13:48, 21 February 2008
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Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi
Overview
Tyvelose is a unique 3,6-dideoxyhexose found in the O antigens of some pathogenic species of Yersinia and Salmonella. It is produced via a complex biochemical pathway that employs CDP-D-glucose as the starting ligand. CDP-D-glucose 4,6-dehydratase catalyzes the first irreversible step in the synthesis of this 3,6-dideoxysugar by converting CDP-D-glucose to CDP-4-keto-6-deoxyglucose via an NAD+ -dependent intramolecular oxidation-reduction reaction. Here, the cloning, protein purification and X-ray crystallographic analysis of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with the substrate analog CDP-D-xylose are described. Each subunit of the tetrameric enzyme folds into two domains. The N-terminal region contains a Rossmann fold and provides the platform for NAD(H) binding. The C-terminal motif is primarily composed of alpha-helices and houses the binding pocket for the CDP portion of the CDP-D-xylose ligand. The xylose moiety extends into the active-site cleft that is located between the two domains. Key residues involved in anchoring the sugar group to the protein include Ser134, Tyr159, Asn197 and Arg208. Strikingly, Ser134 O gamma and Tyr159 O eta sit within 2.9 A of the 4'-hydroxyl group of xylose. Additionally, the side chains of Asp135 and Lys136 are located at 3.5 and 3.2 A, respectively, from C-5 of xylose. In the structurally related dTDP-D-glucose 4,6-dehydratase, the Asp/Lys pair is replaced with an Asp/Glu couple. On the basis of this investigation, it can be speculated that Tyr159 serves as the catalytic base to abstract the 4'-hydroxyl proton from the sugar and that Asp135 and Lys136 play critical roles in the subsequent dehydration step that leads to the final product.
About this Structure
1WVG is a Single protein structure of sequence from Salmonella enterica subsp. enterica serovar typhi with and as ligands. Active as CDP-glucose 4,6-dehydratase, with EC number 4.2.1.45 Full crystallographic information is available from OCA.
Reference
Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose., Koropatkin NM, Holden HM, Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):365-73. Epub 2005, Mar 24. PMID:15805590
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