PDBsum entry 3hg2

Hydrolase

PDB id: 3hg2

Contents

Protein chain

390 a.a. *

Ligands

NAG-FUC

NAG-NAG-BMA ×2

NAG ×3

SO4 ×3

ACY ×3

GAL

Waters ×329

* Residue conservation analysis

PDB id:

3hg2

Name:

Hydrolase

Title:

Human alpha-galactosidase catalytic mechanism 1. Empty active site

Structure:

Alpha-galactosidase a. Chain: a, b. Synonym: alpha-d-galactoside galactohydrolase, alpha-d-galactosidase a, melibiase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: gla. Expressed in: homo sapiens. Expression_system_taxid: 9606

Resolution:

2.30Å R-factor: 0.178 R-free: 0.202

Authors:

A.I.Guce,N.E.Clark,S.C.Garman

Key ref:

A.I.Guce et al. (2010). Catalytic mechanism of human alpha-galactosidase. J Biol Chem, 285, 3625-3632. PubMed id: 19940122

Date:

13-May-09 Release date: 24-Nov-09

Protein chains

P06280  (AGAL_HUMAN) -  Alpha-galactosidase A from Homo sapiens

Seq: 429 a.a.

Struc: 390 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.22 - alpha-galactosidase.
• Reaction: Melibiose + H₂O = galactose + glucose
• Cofactor: Mg(2+); NAD(+)

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

reference

J Biol Chem 285:3625-3632 (2010)

PubMed id: 19940122

Catalytic mechanism of human alpha-galactosidase.

A.I.Guce, N.E.Clark, E.N.Salgado, D.R.Ivanen, A.A.Kulminskaya, H.Brumer, S.C.Garman.

ABSTRACT

The enzyme alpha-galactosidase (alpha-GAL, also known as alpha-GAL A; E.C. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. Defects in human alpha-GAL lead to the development of Fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues. alpha-GAL is an active target of clinical research: there are currently two treatment options for Fabry disease, recombinant enzyme replacement therapy (approved in the United States in 2003) and pharmacological chaperone therapy (currently in clinical trials). Previously, we have reported the structure of human alpha-GAL, which revealed the overall structure of the enzyme and established the locations of hundreds of mutations that lead to the development of Fabry disease. Here, we describe the catalytic mechanism of the enzyme derived from x-ray crystal structures of each of the four stages of the double displacement reaction mechanism. Use of a difluoro-alpha-galactopyranoside allowed trapping of a covalent intermediate. The ensemble of structures reveals distortion of the ligand into a (1)S(3) skew (or twist) boat conformation in the middle of the reaction cycle. The high resolution structures of each step in the catalytic cycle will allow for improved drug design efforts on alpha-GAL and other glycoside hydrolase family 27 enzymes by developing ligands that specifically target different states of the catalytic cycle. Additionally, the structures revealed a second ligand-binding site suitable for targeting by novel pharmacological chaperones.