1rkx
From Proteopedia
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| - | [[Image:1rkx.gif|left|200px]] | + | [[Image:1rkx.gif|left|200px]] |
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| - | '''Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis''' | + | {{Structure |
| + | |PDB= 1rkx |SIZE=350|CAPTION= <scene name='initialview01'>1rkx</scene>, resolution 1.80Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> | ||
| + | |ACTIVITY= [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] | ||
| + | |GENE= ascB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=633 Yersinia pseudotuberculosis]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1RKX is a [ | + | 1RKX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis Yersinia pseudotuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKX OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structure at 1.8 A resolution of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis., Vogan EM, Bellamacina C, He X, Liu HW, Ringe D, Petsko GA, Biochemistry. 2004 Mar 23;43(11):3057-67. PMID:[http:// | + | Crystal structure at 1.8 A resolution of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis., Vogan EM, Bellamacina C, He X, Liu HW, Ringe D, Petsko GA, Biochemistry. 2004 Mar 23;43(11):3057-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15023057 15023057] |
[[Category: CDP-glucose 4,6-dehydratase]] | [[Category: CDP-glucose 4,6-dehydratase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: sdr]] | [[Category: sdr]] | ||
| - | ''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 13:53:00 2008'' |
Revision as of 11:53, 20 March 2008
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| , resolution 1.80Å | |||||||
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| Ligands: | |||||||
| Gene: | ascB (Yersinia pseudotuberculosis) | ||||||
| Activity: | CDP-glucose 4,6-dehydratase, with EC number 4.2.1.45 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis
Overview
CDP-D-glucose 4,6-dehydratase catalyzes the conversion of CDP-D-glucose to CDP-4-keto-6-deoxyglucose in an NAD(+)-dependent manner. The product of this conversion is a building block for a variety of primary antigenic determinants in bacteria, possibly implicated directly in reactive arthritis. Here, we describe the solution of the high-resolution crystal structure of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis in the resting state. This structure represents the first CDP nucleotide utilizing dehydratase of the short-chain dehydrogenase/reductase (SDR) family to be determined, as well as the first tetrameric structure of the subfamily of SDR enzymes in which NAD(+) undergoes a full reaction cycle. On the basis of a comparison of this structure with structures of homologous enzymes, a chemical mechanism is proposed in which Tyr157 acts as the catalytic base, initiating hydride transfer by abstraction of the proton from the sugar 4'-hydroxyl. Concomitant with the removal of the proton from the 4'-hydroxyl oxygen, the sugar 4'-hydride is transferred to the B face of the NAD(+) cofactor, forming the reduced cofactor and a CDP-4-keto-d-glucose intermediate. A conserved Lys161 most likely acts to position the NAD(+) cofactor so that hydride transfer is favorable and/or to reduce the pK(a) of Tyr157. Following substrate oxidation, we propose that Lys134, acting as a base, would abstract the 5'-hydrogen of CDP-4-keto-D-glucose, priming the intermediate for the spontaneous loss of water. Finally, the resulting Delta(5,6)-glucoseen intermediate would be reduced suprafacially by the cofactor, and reprotonation at C-5' is likely mediated by Lys134.
About this Structure
1RKX is a Single protein structure of sequence from Yersinia pseudotuberculosis. Full crystallographic information is available from OCA.
Reference
Crystal structure at 1.8 A resolution of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis., Vogan EM, Bellamacina C, He X, Liu HW, Ringe D, Petsko GA, Biochemistry. 2004 Mar 23;43(11):3057-67. PMID:15023057
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