Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91453.12 
• Atom Count: 6446 
• Residue Count: 826 
• Unique protein chains: 1

1KCZ

Crystal Structure of beta-methylaspartase from Clostridium tetanomorphum. Mg-complex.

• DOI: 10.2210/pdb1KCZ/pdb

• Classification: LYASE
• Organism(s): Clostridium tetanomorphum
• Expression System: Escherichia coli


• Deposited: 2001-11-12 Released: 2001-12-19 
• Deposition Author(s): Asuncion, M., Blankenfeldt, W., Barlow, J.N., Gani, D., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.175 
• R-Value Work: 0.135 

Literature

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

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

(2002) J.Biol.Chem. 277: 8306-8311

• PubMed: 11748244 
• DOI: 10.1074/jbc.M111180200
• Primary Citation of Related Structures:  
  1KD0


• 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.

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Related Citations: 

• Overexpression, purification, crystallization and data collection of 3-methylaspartase from Clostridium tetanomorphum
  Asuncion, M.,Barlow, J.N.,Pollard, J.,Staines, A.G.,McMahon, S.A.,Blankenfeldt, W.,Gani, D.,Naismith, J.H.
  (2001) Acta Crystallogr.,Sect.D 57: 731




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Organizational Affiliation: 

The Centre for Biomolecular Sciences, The University, St. Andrews, Scotland, United Kingdom KY16 9ST.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
beta-methylaspartase	A, B	413	Clostridium tetanomorphum	Mutation(s): 0  EC: 4.3.1.2
Find proteins for Q05514 (Clostridium tetanomorphum) Go to UniProtKB:  Q05514

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A, B	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.175 
• R-Value Work: 0.135 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 67.016	α = 90.00
b = 108.783	β = 90.00
c = 109.557	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	data scaling
SnB	phasing
SHAKE-N-BAKE	phasing
MOSFLM	data reduction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-12 
• Released Date: 2001-12-19 
• Deposition Author(s): Asuncion, M., Blankenfeldt, W., Barlow, J.N., Gani, D., Naismith, J.H.

Revision History 

• Version 1.0: 2001-12-19
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Refinement description, Version format compliance