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PDBsum entry 2gq3

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
2gq3
Jmol
Contents
Protein chains
720 a.a. *
Ligands
MLT ×2
COA
EPE ×2
Metals
_MG ×4
Waters ×617
* Residue conservation analysis
PDB id:
2gq3
Name: Transferase
Title: Mycobacterium tuberculosis malate synthase in complex with m malate, and coenzyme a
Structure: Malate synthase g. Chain: a, b. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: glcb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.174     R-free:   0.244
Authors: D.M.Anstrom,S.J.Remington
Key ref:
D.M.Anstrom and S.J.Remington (2006). The product complex of M. tuberculosis malate synthase revisited. Protein Sci, 15, 2002-2007. PubMed id: 16877713 DOI: 10.1110/ps.062300206
Date:
19-Apr-06     Release date:   15-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P9WK17  (MASZ_MYCTU) -  Malate synthase G
Seq:
Struc:
 
Seq:
Struc:
741 a.a.
720 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.3.9  - Malate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Glyoxylate Cycle
      Reaction: Acetyl-CoA + H2O + glyoxylate = (S)-malate + CoA
Acetyl-CoA
+ H(2)O
+ glyoxylate
=
(S)-malate
Bound ligand (Het Group name = MLT)
corresponds exactly
+
CoA
Bound ligand (Het Group name = COA)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   5 terms 
  Biological process     glyoxylate cycle   2 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1110/ps.062300206 Protein Sci 15:2002-2007 (2006)
PubMed id: 16877713  
 
 
The product complex of M. tuberculosis malate synthase revisited.
D.M.Anstrom, S.J.Remington.
 
  ABSTRACT  
 
Enzymes of the glyoxylate shunt have been implicated as virulence factors in several pathogenic organisms, notably Mycobacterium tuberculosis and Candida albicans. Malate synthase has thus emerged as a promising target for design of anti-microbial agents. For this effort, it is essential to have reliable models for enzyme:substrate complexes. A 2.7 Angstroms resolution crystal structure for M. tuberculosis malate synthase in the ternary complex with magnesium, malate, and coenzyme A has been previously described. However, some unusual aspects of malate and Mg(++) binding prompted an independent determination of the structure at 2.3 Angstroms resolution, in the presence of saturating concentrations of malate. The electron density map of the complex reveals the position and conformation of coenzyme A to be unchanged from that found in the previous study. However, the coordination of Mg(++) and orientation of bound malate within the active site are different. The revised position of bound malate is consistent with a reaction mechanism that does not require reorientation of the electrophilic substrate during the catalytic cycle, while the revised Mg(++) coordination is octahedral, as expected. The results should be useful in the design of malate synthase inhibitors.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (A) Stereo view of a ball-and-stick model of the active site of tbMSG superimposed on a portion of a sA-weighted Fo-Fc omit electron density map contoured at 3.5 s. Malate, magnesium, and the two water molecules coordinating magnesium were omitted for the purpose of phase calculation. (B) Stereo view showing magnesium coordination and position of pyruvate and the acetyl terminus of acetyl-CoA as reported by Anstrom et al. (2003; PDB ID 1P7T). (C) Stereo image of magnesium coordination and malate position as reported by Smith et al. (2003; PDB ID 1N8W). In all figures relevant hydrogen bonds and salt bridges are shown as black dashed lines, while potential electrostatic clashes are shown as red dashed lines. In A and C, numbering is for mTB malate synthase, whereas in B, numbering is that of E. coli malate synthase G.
 
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2006, 15, 2002-2007) copyright 2006.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20306314 R.Kumar, and V.Bhakuni (2010).
A functionally active dimer of Mycobacterium tuberculosis Malate synthase G.
  Eur Biophys J, 39, 1557-1562.  
19549344 B.Roucourt, N.Minnebo, P.Augustijns, K.Hertveldt, G.Volckaert, and R.Lavigne (2009).
Biochemical characterization of malate synthase G of P. aeruginosa.
  BMC Biochem, 10, 20.  
18714089 J.R.Lohman, A.C.Olson, and S.J.Remington (2008).
Atomic resolution structures of Escherichia coli and Bacillus anthracis malate synthase A: comparison with isoform G and implications for structure-based drug discovery.
  Protein Sci, 17, 1935-1945.
PDB codes: 3cux 3cuz 3cv1 3cv2
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