1rkx
From Proteopedia
(New page: 200px<br /><applet load="1rkx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rkx, resolution 1.80Å" /> '''Crystal Structure at...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1rkx.gif|left|200px]]<br /><applet load="1rkx" size=" | + | [[Image:1rkx.gif|left|200px]]<br /><applet load="1rkx" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1rkx, resolution 1.80Å" /> | caption="1rkx, resolution 1.80Å" /> | ||
'''Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis'''<br /> | '''Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis'''<br /> | ||
==Overview== | ==Overview== | ||
| - | CDP-D-glucose 4,6-dehydratase catalyzes the conversion of CDP-D-glucose to | + | 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== | ==About this Structure== | ||
| - | 1RKX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis Yersinia pseudotuberculosis] with NAD as [http://en.wikipedia.org/wiki/ligand ligand]. 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:// | + | 1RKX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis Yersinia pseudotuberculosis] with <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1RKX OCA]. |
==Reference== | ==Reference== | ||
| Line 16: | Line 16: | ||
[[Category: Bellamacina, C.]] | [[Category: Bellamacina, C.]] | ||
[[Category: He, X.]] | [[Category: He, X.]] | ||
| - | [[Category: Liu, H | + | [[Category: Liu, H W.]] |
| - | [[Category: Petsko, G | + | [[Category: Petsko, G A.]] |
[[Category: Ringe, D.]] | [[Category: Ringe, D.]] | ||
| - | [[Category: Vogan, E | + | [[Category: Vogan, E M.]] |
[[Category: NAD]] | [[Category: NAD]] | ||
[[Category: cdp glucose dehydratase]] | [[Category: cdp glucose dehydratase]] | ||
| Line 25: | Line 25: | ||
[[Category: sdr]] | [[Category: sdr]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:51:59 2008'' |
Revision as of 12:52, 21 February 2008
|
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 with as ligand. Active as CDP-glucose 4,6-dehydratase, with EC number 4.2.1.45 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
Page seeded by OCA on Thu Feb 21 14:51:59 2008
