PDBsum entry 2i3c

Hydrolase

PDB id: 2i3c

Contents

Protein chain

302 a.a. *

Ligands

PO4 ×8

Metals

_ZN ×2

Waters ×36

* Residue conservation analysis

PDB id:

2i3c

Name:

Hydrolase

Title:

Crystal structure of an aspartoacylase from homo sapiens

Structure:

Aspartoacylase. Chain: a, b. Synonym: aminoacylase-2, acy-2. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: aspa, acy2, asp. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.80Å R-factor: 0.197 R-free: 0.243

Authors:

E.Bitto,G.E.Wesenberg,G.N.Phillips Jr.,J.G.Mccoy,C.A.Bingman,Center For Eukaryotic Structural Genomics (Cesg)

Key ref:

E.Bitto et al. (2007). Structure of aspartoacylase, the brain enzyme impaired in Canavan disease. Proc Natl Acad Sci U S A, 104, 456-461. PubMed id: 17194761 DOI: 10.1073/pnas.0607817104

Date:

17-Aug-06 Release date: 29-Aug-06

Protein chains

P45381  (ACY2_HUMAN) -  Aspartoacylase from Homo sapiens

Seq: 313 a.a.

Struc: 302 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.15 - aspartoacylase.
• Reaction: an N-acyl-L-aspartate + H2O = a carboxylate + L-aspartate

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

reference

DOI no: 10.1073/pnas.0607817104

Proc Natl Acad Sci U S A 104:456-461 (2007)

PubMed id: 17194761

Structure of aspartoacylase, the brain enzyme impaired in Canavan disease.

E.Bitto, C.A.Bingman, G.E.Wesenberg, J.G.McCoy, G.N.Phillips.

ABSTRACT

Aspartoacylase catalyzes hydrolysis of N-acetyl-l-aspartate to aspartate and acetate in the vertebrate brain. Deficiency in this activity leads to spongiform degeneration of the white matter of the brain and is the established cause of Canavan disease, a fatal progressive leukodystrophy affecting young children. We present crystal structures of recombinant human and rat aspartoacylase refined to 2.8- and 1.8-A resolution, respectively. The structures revealed that the N-terminal domain of aspartoacylase adopts a protein fold similar to that of zinc-dependent hydrolases related to carboxypeptidases A. The catalytic site of aspartoacylase shows close structural similarity to those of carboxypeptidases despite only 10-13% sequence identity between these proteins. About 100 C-terminal residues of aspartoacylase form a globular domain with a two-stranded beta-sheet linker that wraps around the N-terminal domain. The long channel leading to the active site is formed by the interface of the N- and C-terminal domains. The C-terminal domain is positioned in a way that prevents productive binding of polypeptides in the active site. The structures revealed that residues 158-164 may undergo a conformational change that results in opening and partial closing of the channel entrance. We hypothesize that the catalytic mechanism of aspartoacylase is closely analogous to that of carboxypeptidases. We identify residues involved in zinc coordination, and propose which residues may be involved in substrate binding and catalysis. The structures also provide a structural framework necessary for understanding the deleterious effects of many missense mutations of human aspartoacylase.

Selected figure(s)

Figure 1.
Fig. 1. Ribbon diagrams of the rASPA monomer and dimer. (A) N-domain of rASPA is color-coded in cyan and red. C-domain is color-coded in yellow and green. Residues His-21, Gly-22, Glu-24, Asn-54, Arg-63, Asn-70, Arg-71, Phe-73, Asp-114, His-116, and Glu-178 (blue sticks) are highly conserved in the AstE-AspA family and delineate the active site. Zn^2+ is shown as a pink sphere. (B) The rASPA dimer observed in the asymmetric unit of the rASPA crystals is shown in ribbon representation. Both the N-domain (red) and C-domain (green) of the rASPA monomers are involved in formation of the dimer interface. Residues His-21, Glu-24, and His-116 (blue sticks) coordinate Zn^2+ (pink sphere).

Figure 4.
Fig. 4. Proposed mechanism of action of ASPA.

Figures were selected by an automated process.