1RDF

G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate

Summary for 1RDF

• Entry DOI: 10.2210/pdb1rdf/pdb
• Related: 1FEZ 1LVH
• Descriptor: phosphonoacetaldehyde hydrolase, MAGNESIUM ION, ETHANESULFONIC ACID, ... (4 entities in total)
• Functional Keywords: haloacid dehalogenase, specificity loop, phosphonatase, schiff-base, hydrolase
• Biological source: Bacillus cereus
• Total number of polymer chains: 6
• Total formula weight: 184107.56

Authors

Lahiri, S.D.,Zhang, G.,Dunaway-Mariano, D.,Allen, K.N. (deposition date: 2003-11-05, release date: 2004-08-31, Last modification date: 2023-08-23)

Primary citation

Lahiri, S.D.,Zhang, G.,Dai, J.,Dunaway-Mariano, D.,Allen, K.N.
Analysis of the substrate specificity loop of the HAD superfamily cap domain
Biochemistry, 43:2812-2820, 2004

PubMed Abstract: The haloacid dehalogenase (HAD) superfamily includes a variety of enzymes that catalyze the cleavage of substrate C-Cl, P-C, and P-OP bonds via nucleophilic substitution pathways. All members possess the alpha/beta core domain, and many also possess a small cap domain. The active site of the core domain is formed by four loops (corresponding to sequence motifs 1-4), which position substrate and cofactor-binding residues as well as the catalytic groups that mediate the "core" chemistry. The cap domain is responsible for the diversification of chemistry within the family. A tight beta-turn in the helix-loop-helix motif of the cap domain contains a stringently conserved Gly (within sequence motif 5), flanked by residues whose side chains contribute to the catalytic site formed at the domain-domain interface. To define the role of the conserved Gly in the structure and function of the cap domain loop of the HAD superfamily members phosphonoacetaldehyde hydrolase and beta-phosphoglucomutase, the Gly was mutated to Pro, Val, or Ala. The catalytic activity was severely reduced in each mutant. To examine the impact of Gly substitution on loop 5 conformation, the X-ray crystal structure of the Gly50Pro phosphonoacetaldehyde hydrolase mutant was determined. The altered backbone conformation at position 50 had a dramatic effect on the spatial disposition of the side chains of neighboring residues. Lys53, the Schiff Base forming lysine, had rotated out of the catalytic site and the side chain of Leu52 had moved to fill its place. On the basis of these studies, it was concluded that the flexibility afforded by the conserved Gly is critical to the function of loop 5 and that it is a marker by which the cap domain substrate specificity loop can be identified within the amino acid sequence of HAD family members.

PubMed: 15005616
DOI: 10.1021/bi0356810

Experimental method

X-RAY DIFFRACTION (2.8 Å)