PDBsum entry: 1swv

Hydrolase

PDB id: 1swv

Contents

Protein chains

257 a.a. *

Metals

_MG ×2

Waters ×232

* Residue conservation analysis

PDB id:

1swv

Name:

Hydrolase

Title:

Crystal structure of the d12a mutant of phosphonoacetaldehyde hydrolase complexed with magnesium

Structure:

Phosphonoacetaldehyde hydrolase. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Bacillus cereus. Organism_taxid: 1396. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.216 R-free: 0.278

Authors:

G.Zhang,M.C.Morais,J.Dai,W.Zhang,D.Dunaway-Mariano,K.N.Allen

Key ref:

G.Zhang et al. (2004). Investigation of metal ion binding in phosphonoacetaldehyde hydrolase identifies sequence markers for metal-activated enzymes of the HAD enzyme superfamily. Biochemistry, 43, 4990-4997. PubMed id: 15109258 DOI: 10.1021/bi036309n

Date:

30-Mar-04 Release date: 05-Oct-04

Protein chains

O31156  (PHNX_BACCE) -  Phosphonoacetaldehyde hydrolase

Seq: 264 a.a.

Struc: 257 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.11.1.1 - Phosphonoacetaldehyde hydrolase.
• Reaction: Phosphonoacetaldehyde + H₂O = acetaldehyde + phosphate
• Cofactor: Magnesium

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (1 term)
• Biochemical function: catalytic activity (5 terms)

reference

DOI no: 10.1021/bi036309n

Biochemistry 43:4990-4997 (2004)

PubMed id: 15109258

Investigation of metal ion binding in phosphonoacetaldehyde hydrolase identifies sequence markers for metal-activated enzymes of the HAD enzyme superfamily.

G.Zhang, M.C.Morais, J.Dai, W.Zhang, D.Dunaway-Mariano, K.N.Allen.

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.