2ORM

Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori.

2ORM の概要

• エントリーDOI: 10.2210/pdb2orm/pdb
• 関連するPDBエントリー: 1AAG 1BJP 1GYJ 2OP8
• 分子名称: Probable tautomerase HP0924 (2 entities in total)
• 機能のキーワード: homohexamer, 4-ot, 4-oxalocrotonate tautomerase homologue, isomerase
• 由来する生物種: Helicobacter pylori
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 44336.29

構造登録者

Hackert, M.L.,Whitman, C.P.,Almrud, J.J.,Dasgupta, R.,Czerwinski, R.M.,Kern, A.D. (登録日: 2007-02-03, 公開日: 2008-02-12, 最終更新日: 2023-08-30)

主引用文献

Almrud, J.J.,Dasgupta, R.,Czerwinski, R.M.,Kern, A.D.,Hackert, M.L.,Whitman, C.P.
Kinetic and structural characterization of DmpI from Helicobacter pylori and Archaeoglobus fulgidus, two 4-oxalocrotonate tautomerase family members.
Bioorg.Chem., 38:252-259, 2010

PubMed Abstract: The tautomerase superfamily consists of structurally homologous proteins that are characterized by a β-α-β fold and a catalytic amino-terminal proline. 4-Oxalocrotonate tautomerase (4-OT) family members have been identified and categorized into five subfamilies on the basis of multiple sequence alignments and the conservation of key catalytic and structural residues. Representative members from two subfamilies have been cloned, expressed, purified, and subjected to kinetic and structural characterization. The crystal structure of DmpI from Helicobacter pylori (HpDmpI), a 4-OT homolog in subfamily 3, has been determined to high resolution (1.8Å and 2.1Å) in two different space groups. HpDmpI is a homohexamer with an active site cavity that includes Pro-1, but lacks the equivalent of Arg-11 and Arg-39 found in 4-OT. Instead, the side chain of Lys-36 replaces that of Arg-11 in a manner similar to that observed in the trimeric macrophage migration inhibitory factor (MIF), which is the title protein of another family in the superfamily. The electrostatic surface of the active site is also quite different and suggests that HpDmpI might prefer small, monoacid substrates. A kinetic analysis of the enzyme is consistent with the structural analysis, but a biological role for the enzyme remains elusive. The crystal structure of DmpI from Archaeoglobus fulgidus (AfDmpI), a 4-OT homolog in subfamily-4, has been determined to 2.4Å resolution. AfDmpI is also a homohexamer, with a proposed active site cavity that includes Pro-1, but lacks any other residues that are readily identified as catalytic ones related to 4-OT activity. Indeed, the electrostatic potential of the active site differs significantly in that it is mostly neutral, in contrast to the usual electropositive features found in other 4-OT family members, suggesting that AfDmpI might accommodate hydrophobic substrates. A kinetic analysis has been carried out, but does not provide any clues about the type of reaction the enzyme might catalyze.

PubMed: 20709352
DOI: 10.1016/j.bioorg.2010.07.002

実験手法

X-RAY DIFFRACTION (2.1 Å)