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| - | [[Image:2zea.jpg|left|200px]] | + | #REDIRECT [[3vdq]] This PDB entry is obsolete and replaced by 3vdq |
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| - | {{STRUCTURE_2zea| PDB=2zea | SCENE= }}
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| - | '''Crystal structure of Alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase in complex with NAD+ and acetate'''
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| - | ==Overview==
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| - | D-3-Hydroxybutyrate dehydrogenase, which catalyzes the reversible reaction between D-3-hydroxybutyrate and acetoacetate, has been classified into the short-chain dehydrogenase/reductase family and is a useful marker in the assay of diabetes mellitus and/or ketoacidosis. The enzyme from Alcaligenes faecalis was crystallized in the apo form and in the holo form with acetate as a substrate analogue. The crystal structures of both forms were determined at 2.2 angstroms resolution. The enzyme is a tetramer composed of four subunits assembled with noncrystallographic 222 point symmetry. Each subunit has two domains. The principal domain adopts the Rossmann fold essential for nucleotide binding, which is a common feature of the SDR family. NAD+ is bound in a large cleft in the domain. The pyrophosphate group of NAD+ is covered by the small additional domain, which is supported by two extended arms allowing domain movement. In the catalytic site, a water molecule is trapped by the catalytic Tyr155 and Ser142 residues in the vicinity of the bound NAD+ and acetate. The substrate analogue acetate is bound above the nicotinamide plane. A substrate (D-3-hydroxybutylate) bound model can reasonably be constructed by adding two C atoms into the void space between the water O atom and the methyl group of the acetate, suggesting a substrate-bound state before enzymatic reaction occurs. Based on these structural features, a reaction mechanism has been proposed.
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| - | ==About this Structure==
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| - | 2ZEA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZEA OCA].
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| - | ==Reference==
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| - | The structures of Alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase before and after NAD+ and acetate binding suggest a dynamical reaction mechanism as a member of the SDR family., Hoque MM, Shimizu S, Hossain MT, Yamamoto T, Imamura S, Suzuki K, Tsunoda M, Amano H, Sekiguchi T, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2008 May;64(Pt 5):496-505. Epub 2008, Apr 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18453685 18453685]
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| - | [[Category: 3-hydroxybutyrate dehydrogenase]]
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| - | [[Category: Alcaligenes faecalis]]
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| - | [[Category: Single protein]]
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| - | [[Category: Hoque, M M.]]
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| - | [[Category: Hossain, M T.]]
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| - | [[Category: Shimizu, S.]]
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| - | [[Category: Suzuki, K.]]
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| - | [[Category: Takenaka, A.]]
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| - | [[Category: Yamamoto, T.]]
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| - | [[Category: Hydroxybutyrate dehydrogenase]]
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| - | [[Category: Ketone body]]
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| - | [[Category: Nad dependent enzyme]]
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| - | [[Category: Oxidoreductase]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 4 09:53:51 2008''
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