1SWV

Crystal structure of the D12A mutant of phosphonoacetaldehyde hydrolase complexed with magnesium

1SWV の概要

• エントリーDOI: 10.2210/pdb1swv/pdb
• 関連するPDBエントリー: 1FEZ
• 分子名称: phosphonoacetaldehyde hydrolase, MAGNESIUM ION (3 entities in total)
• 機能のキーワード: had enzyme superfamily, phosphonotase, phosphonoacetaldehyde, metal binding, hydrolase
• 由来する生物種: Bacillus cereus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 60952.73

構造登録者

Zhang, G.,Morais, M.C.,Dai, J.,Zhang, W.,Dunaway-Mariano, D.,Allen, K.N. (登録日: 2004-03-30, 公開日: 2004-10-05, 最終更新日: 2023-08-23)

主引用文献

Zhang, G.,Morais, M.C.,Dai, J.,Zhang, W.,Dunaway-Mariano, D.,Allen, K.N.
Investigation of metal ion binding in phosphonoacetaldehyde hydrolase identifies sequence markers for metal-activated enzymes of the HAD enzyme superfamily
Biochemistry, 43:4990-4997, 2004

PubMed Abstract: The 2-haloalkanoic acid dehalogenase (HAD) family, which contains both carbon and phosphoryl transferases, is one of the largest known enzyme superfamilies. HAD members conserve an alpha,beta-core domain that frames the four-loop active-site platform. Each loop contributes one or more catalytic groups, which function in mediating the core chemistry (i.e., group transfer). In this paper, we provide evidence that the number of carboxylate residues on loop 4 and their positions (stations) on the loop are determinants, and therefore reliable sequence markers, for metal ion activation among HAD family members. Using this predictor, we conclude that the vast majority of the HAD members utilize a metal cofactor. Analysis of the minimum requirements for metal cofactor binding was carried out using Mg(II)-activated Bacillus cereus phosphonoacetaldehyde hydrolase (phosphonatase) as an experimental model for metal-activated HAD members. Mg(II) binding occurs via ligation to the loop 1 Asp12 carboxylate and Thr14 backbone carbonyl and to the loop 4 Asp186 carboxylate. The loop 4 Asp190 forms a hydrogen bond to the Mg(II) water ligand. X-ray structure determination of the D12A mutant in the presence of the substrate phosphonoacetaldehyde showed that replacement of the loop 1 Asp, common to all HAD family members, with Ala shifts the position of Mg(II), thereby allowing innersphere coordination to Asp190 and causing a shift in the position of the substrate. Kinetic analysis of the loop 4 mutants showed that Asp186 is essential to cofactor binding while Asp190 simply enhances it. Within the phosphonatase subfamily, Asp186 is stringently conserved, while either position 185 or position 190 is used to position the second loop 4 Asp residue. Retention of a high level of catalytic activity in the G185D/D190G phosphonatase mutant demonstrated the plasticity of the metal binding loop, reflected in the variety of combinations in positioning of two or three Asp residues along the seven-residue motif of the 2700 potential HAD sequences that were examined.

PubMed: 15109258
DOI: 10.1021/bi036309n

実験手法

X-RAY DIFFRACTION (2.3 Å)