spacer
spacer

PDBsum entry 1kko
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Lyase PDB id
1kko

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
411 a.a. *
Ligands
SO4
Waters ×2203
* Residue conservation analysis
PDB id:
1kko
Name: Lyase
Title: Crystal structure of citrobacter amalonaticus methylaspartate ammonia lyase
Structure: 3-methylaspartate ammonia-lyase. Chain: a, b. Engineered: yes
Source: Citrobacter amalonaticus. Organism_taxid: 35703. Gene: mal. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.33Å     R-factor:   0.162     R-free:   0.191
Authors: C.W.Levy,P.A.Buckley,S.Sedelnikova,Y.Kato,Y.Asano,D.W.Rice,P.J.Baker
Key ref:
C.W.Levy et al. (2002). Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase. Structure, 10, 105-113. PubMed id: 11796115 DOI: 10.1016/S0969-2126(01)00696-7
Date:
10-Dec-01     Release date:   30-Jan-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O66145  (MAAL_CITAM) -  Methylaspartate ammonia-lyase from Citrobacter amalonaticus
Seq:
Struc: 		413 a.a.
411 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.3.1.2  - methylaspartate ammonia-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (2S,3S)-3-methyl-L-aspartate = mesaconate + NH4+
(2S,3S)-3-methyl-L-aspartate
 = mesaconate
 + NH4(+)
      Cofactor: Cob(II)alamin
Cob(II)alamin
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/S0969-2126(01)00696-7 Structure 10:105-113 (2002)
PubMed id: 11796115  
 
 
Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase.
C.W.Levy, P.A.Buckley, S.Sedelnikova, Y.Kato, Y.Asano, D.W.Rice, P.J.Baker.
 
  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.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. A Schematic of the Proposed Reaction Mechanism of MALThe 3-proton of (2S,3S)-3-methyl aspartic acid is abstracted by Lys-331 acting as a base to give the enolic intermediate shown in the middle panel. The negative charge on the aci-carboxylate is stabilized by the metal ion and possibly by His-194 acting as an electrophile. The enolic intermediate collapses with the elimination of ammonia to yield mesaconic acid (right hand panel).
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 105-113) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19670200 H.Raj, B.Weiner, V.P.Veetil, C.R.Reis, W.J.Quax, D.B.Janssen, B.L.Feringa, and G.J.Poelarends (2009).
Alteration of the diastereoselectivity of 3-methylaspartate ammonia lyase by using structure-based mutagenesis.
  Chembiochem, 10, 2236-2245.  
16704345 W.Buckel, and B.T.Golding (2006).
Radical enzymes in anaerobes.
  Annu Rev Microbiol, 60, 27-49.  
15857789 Y.Asano, I.Kira, and K.Yokozeki (2005).
Alteration of substrate specificity of aspartase by directed evolution.
  Biomol Eng, 22, 95.  
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
12842039 B.N.Chaudhuri, M.R.Sawaya, C.Y.Kim, G.S.Waldo, M.S.Park, T.C.Terwilliger, and T.O.Yeates (2003).
The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.
  Structure, 11, 753-764.
PDB code: 1oy0
12930985 T.Kajander, L.Lehtiö, M.Schlömann, and A.Goldman (2003).
The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function.
  Protein Sci, 12, 1855-1864.
PDB code: 1nu5
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

spacer
spacer