PDBsum entry 1b93

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protein ligands Protein-protein interface(s) links
Lyase PDB id
Protein chains
148 a.a. *
FMT ×7
Waters ×217
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Methylglyoxal synthase from escherichia coli
Structure: Protein (methylglyoxal synthase). Chain: a, b, c. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: le392. Cellular_location: cytoplasm. Gene: mgsa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PDB file)
1.90Å     R-factor:   0.181     R-free:   0.202
Authors: D.Saadat,D.H.T.Harrison
Key ref:
D.Saadat and D.H.Harrison (1999). The crystal structure of methylglyoxal synthase from Escherichia coli. Structure, 7, 309-317. PubMed id: 10368300 DOI: 10.1016/S0969-2126(99)80041-0
19-Feb-99     Release date:   16-Mar-99    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A731  (MGSA_ECOLI) -  Methylglyoxal synthase
152 a.a.
148 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Methylglyoxal synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Glycerone phosphate = methylglyoxal + phosphate
Glycerone phosphate
= methylglyoxal
Bound ligand (Het Group name = PO4)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     methylglyoxal biosynthetic process   1 term 
  Biochemical function     lyase activity     2 terms  


DOI no: 10.1016/S0969-2126(99)80041-0 Structure 7:309-317 (1999)
PubMed id: 10368300  
The crystal structure of methylglyoxal synthase from Escherichia coli.
D.Saadat, D.H.Harrison.
BACKGROUND: The reaction mechanism of methylglyoxal synthase (MGS) is believed to be similar to that of triosephosphate isomerase (TIM). Both enzymes utilise dihydroxyacetone phosphate (DHAP) to form an enediol(ate) phosphate intermediate as the first step of their reaction pathways. However, the second catalytic step in the MGS reaction pathway is characterized by the elimination of phosphate and collapse of the enediol(ate) to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate. RESULTS: The crystal structure of MGS bound to formate and substoichiometric amounts of phosphate in the space group P6522 has been determined at 1.9 A resolution. This structure shows that the enzyme is a homohexamer composed of interacting five-stranded beta/alpha proteins, rather than the hallmark alpha/beta barrel structure of TIM. The conserved residues His19, Asp71, and His98 in each of the three monomers in the asymmetric unit bind to a formate ion that is present in the crystallization conditions. Differences in the three monomers in the asymmetric unit are localized at the mouth of the active site and can be ascribed to the presence or absence of a bound phosphate ion. CONCLUSIONS: In agreement with site-directed mutagenesis and mechanistic enzymology, the structure suggests that Asp71 acts as the catalytic base. Further, Asp20 and Asp101 are involved in intersubunit salt bridges. These salt bridges may provide a pathway for transmitting allosteric information.
  Selected figure(s)  
Figure 1.
Figure 1. Reaction mechanism for MGS.
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 309-317) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20419481 M.Pazhang, K.Khajeh, S.M.Asghari, H.Falahati, and H.Naderi-Manesh (2010).
Cloning, expression, and characterization of a novel methylglyoxal synthase from Thermus sp. strain GH5.
  Appl Biochem Biotechnol, 162, 1519-1528.  
20686683 R.Potestio, C.Micheletti, and H.Orland (2010).
Knotted vs. unknotted proteins: evidence of knot-promoting loops.
  PLoS Comput Biol, 6, e1000864.  
19622869 P.Gayathri, M.Banerjee, A.Vijayalakshmi, H.Balaram, P.Balaram, and M.R.Murthy (2009).
Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site.
  Acta Crystallogr D Biol Crystallogr, 65, 847-857.
PDB codes: 2vfd 2vfe 2vff 2vfg 2vfh 2vfi
17419878 Y.Wei, J.Ko, L.F.Murga, and M.J.Ondrechen (2007).
Selective prediction of interaction sites in protein structures with THEMATICS.
  BMC Bioinformatics, 8, 119.  
16146579 D.M.Standley, H.Toh, and H.Nakamura (2005).
GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures.
  BMC Bioinformatics, 6, 221.  
16100107 K.E.Christensen, I.A.Mirza, A.M.Berghuis, and R.E.Mackenzie (2005).
Magnesium and phosphate ions enable NAD binding to methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase.
  J Biol Chem, 280, 34316-34323.
PDB code: 1zn4
12069781 G.Labesse, D.Douguet, L.Assairi, and A.M.Gilles (2002).
Diacylglyceride kinases, sphingosine kinases and NAD kinases: distant relatives of 6-phosphofructokinases.
  Trends Biochem Sci, 27, 273-275.  
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 codes are shown on the right.