1KD0

Crystal Structure of beta-methylaspartase from Clostridium tetanomorphum. Apo-structure.

Summary for 1KD0

• Entry DOI: 10.2210/pdb1kd0/pdb
• Related: 1kcz
• Descriptor: beta-methylaspartase, 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: beta zigzag, alpha/beta-barrel, lyase
• Biological source: Clostridium tetanomorphum
• Total number of polymer chains: 2
• Total formula weight: 92902.92

Authors

Asuncion, M.,Blankenfeldt, W.,Barlow, J.N.,Gani, D.,Naismith, J.H. (deposition date: 2001-11-12, release date: 2001-12-19, Last modification date: 2024-10-16)

Primary citation

Asuncion, M.,Blankenfeldt, W.,Barlow, J.N.,Gani, D.,Naismith, J.H.
The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step.
J.Biol.Chem., 277:8306-8311, 2002

PubMed 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.

PubMed: 11748244
DOI: 10.1074/jbc.M111180200

Experimental method

X-RAY DIFFRACTION (1.9 Å)