1KCZ

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

PDB DOI: https://doi.org/10.2210/pdb1KCZ/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.175
R-Value Work: 0.135
R-Value Observed: 0.137

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M111180200
Primary Citation of Related Structures:
1KCZ, 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 91.45 kDa
Atom Count: 7,293
Modelled Residue Count: 826
Deposited Residue Count: 826
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-methylaspartase	A, B	413	Clostridium tetanomorphum	Mutation(s): 1 EC: 4.3.1.2
UniProt
Find proteins for Q05514 (Clostridium tetanomorphum) Explore Q05514 Go to UniProtKB: Q05514
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05514
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.175
R-Value Work: 0.135
R-Value Observed: 0.137
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.016	α = 90
b = 108.783	β = 90
c = 109.557	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2001-12-19

Deposition Author(s):

Revision History (Full details and data files)

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