PDBsum entry 1kd0

Lyase

PDB id: 1kd0

Contents

Protein chains

413 a.a. *

Ligands

EDO ×2

Waters ×659

* Residue conservation analysis

PDB id:

1kd0

Name:

Lyase

Title:

Crystal structure of beta-methylaspartase from clostridium tetanomorphum. Apo-structure.

Structure:

Beta-methylaspartase. Chain: a, b. Synonym: methylaspartate ammonia-lyase. Engineered: yes

Source:

Clostridium tetanomorphum. Organism_taxid: 1553. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.178 R-free: 0.222

Authors:

M.Asuncion,W.Blankenfeldt,J.N.Barlow,D.Gani,J.H.Naismith

Key ref:

M.Asuncion et al. (2002). The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step. J Biol Chem, 277, 8306-8311. PubMed id: 11748244 DOI: 10.1074/jbc.M111180200

Date:

12-Nov-01 Release date: 19-Dec-01

Protein chains

Q05514  (MAAL_CLOTT) -  Methylaspartate ammonia-lyase from Clostridium tetanomorphum

Seq: 413 a.a.

Struc: 413 a.a.

Enzyme reactions

• Enzyme class: E.C.4.3.1.2 - methylaspartate ammonia-lyase.
• Reaction: (2S,3S)-3-methyl-L-aspartate = mesaconate + NH4⁺
• Cofactor: Cob(II)alamin

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

Added reference

DOI no: 10.1074/jbc.M111180200

J Biol Chem 277:8306-8311 (2002)

PubMed id: 11748244

The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step.

M.Asuncion, W.Blankenfeldt, J.N.Barlow, D.Gani, J.H.Naismith.

ABSTRACT

Methylaspartate ammonia-lyase (3-methylaspartase, MAL; EC ) catalyzes the reversible anti elimination of ammonia from L-threo-(2S,3S)-3-methylaspartic acid to give mesaconic acid. This reaction lies on the main catabolic pathway for glutamate in Clostridium tetanomorphum. MAL requires monovalent and divalent cation cofactors for full catalytic activity. The enzyme has attracted interest because of its potential use as a biocatalyst. The structure of C. tetanomorphum MAL has been solved to 1.9-A resolution by the single-wavelength anomalous diffraction method. A divalent metal ion complex of the protein has also been determined. MAL is a homodimer with each monomer consisting of two domains. One is an alpha/beta-barrel, and the other smaller domain is mainly beta-strands. The smaller domain partially occludes the C terminus of the barrel and forms a large cleft. The structure identifies MAL as belonging to the enolase superfamily of enzymes. The metal ion site is located in a large cleft between the domains. Potential active site residues have been identified based on a combination of their proximity to a metal ion site, molecular modeling, and sequence homology. In common with all members of the enolase superfamily, the carboxylic acid of the substrate is co-ordinated by the metal ions, and a proton adjacent to a carboxylic acid group of the substrate is abstracted by a base. In MAL, it appears that Lys(331) removes the alpha-proton of methylaspartic acid. This motif is the defining mechanistic characteristic of the enolase superfamily of which all have a common fold. The degree of structural conservation is remarkable given only four residues are absolutely conserved.

Selected figure(s)

Figure 1.
Fig. 1. The reaction catalyzed by methylaspartase. The reverse reaction is both stereo- and regiospecific. Harnessing this reaction for organic synthesis would provide a new route to homochiral aspartic acids.

Figure 4.
Fig. 4. The model of MAL with its substrate at the active site. The residues that bind the metal ion are shown along with those inferred to be the catalytic base (Lys331) and substrate recognition (Arg80). His194, which may be important in deprotonating the other diastereomer is also shown. MASP, methylaspartate. The original position of the side chains of Arg80 and Lys331 are shown in gray.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 8306-8311) copyright 2002.

Figures were selected by an automated process.