1KKO | pdb_00001kko

CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMMONIA LYASE

• PDB DOI: https://doi.org/10.2210/pdb1KKO/pdb

• Classification: LYASE
• Organism(s): Citrobacter amalonaticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-12-10 Released: 2002-01-30 
• Deposition Author(s): Levy, C.W., Buckley, P.A., Sedelnikova, S., Kato, Y., Asano, Y., Rice, D.W., Baker, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 
  0.191 (Depositor) 
• R-Value Work: 
  0.161 (Depositor) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase.

Levy, C.W., Buckley, P.A., Sedelnikova, S., Kato, Y., Asano, Y., Rice, D.W., Baker, P.J.

(2002) Structure 10: 105-113

• PubMed: 11796115 
• DOI: https://doi.org/10.1016/s0969-2126(01)00696-7
• Primary Citation Related Structures: 
  1KKO, 1KKR


• PubMed Abstract: 
  

  Methylaspartate ammonia lyase (MAL) catalyzes the magnesium-dependent reversible alpha,beta-elimination of ammonia from L-threo-(2S,3S)-3-methylaspartic acid to mesaconic acid. The 1.3 A MAD crystal structure of the dimeric Citrobacter amalonaticus MAL shows that each subunit comprises two domains, one of which adopts the classical TIM barrel fold, with the active site at the C-terminal end of the barrel. Despite very low sequence similarity, the structure of MAL is closely related to those of representative members of the enolase superfamily, indicating that the mechanism of MAL involves the initial abstraction of a proton alpha to the 3-carboxyl of (2S,3S)-3-methylasparic acid to yield an enolic intermediate. This analysis resolves the conflict that had linked MAL to the histidine and phenylalanine ammonia lyase family of enzymes.

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Organizational Affiliation: 
• Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 92.08 kDa 
• Atom Count: 8,530 
• Modeled Residue Count: 822 
• Deposited Residue Count: 826 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-METHYLASPARTATE AMMONIA-LYASE	A, B	413	Citrobacter amalonaticus	Mutation(s): 10  Gene Names: MAL EC: 4.3.1.2
UniProt
Find proteins for O66145 (Citrobacter amalonaticus) Explore O66145  Go to UniProtKB:  O66145

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.191 (Depositor) 
• R-Value Work:  0.161 (Depositor) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.339	α = 90
b = 237.362	β = 90
c = 65.806	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
REFMAC	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-30 
Deposition Author(s): Levy, C.W., Buckley, P.A., Sedelnikova, S., Kato, Y., Asano, Y., Rice, D.W., Baker, P.J.

Revision History  

• Version 1.0: 2002-01-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary