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PDBsum entry 1bh5

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1bh5
Jmol
Contents
Protein chain
177 a.a. *
Ligands
GTX ×4
Metals
_ZN ×4
Waters ×507
* Residue conservation analysis
PDB id:
1bh5
Name: Lyase
Title: Human glyoxalase i q33e, e172q double mutant
Structure: Lactoylglutathione lyase. Chain: a, b, c, d. Synonym: glyoxalase i. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.190     R-free:   0.250
Authors: A.D.Cameron,T.A.Jones
Key ref:
M.Ridderström et al. (1998). Involvement of an active-site Zn2+ ligand in the catalytic mechanism of human glyoxalase I. J Biol Chem, 273, 21623-21628. PubMed id: 9705294 DOI: 10.1074/jbc.273.34.21623
Date:
13-Jun-98     Release date:   04-Nov-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q04760  (LGUL_HUMAN) -  Lactoylglutathione lyase
Seq:
Struc:
184 a.a.
177 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.4.1.5  - Lactoylglutathione lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (R)-S-lactoylglutathione = glutathione + methylglyoxal
(R)-S-lactoylglutathione
Bound ligand (Het Group name = GTX)
matches with 82.00% similarity
= glutathione
+ methylglyoxal
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     carbohydrate metabolic process   6 terms 
  Biochemical function     lyase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.273.34.21623 J Biol Chem 273:21623-21628 (1998)
PubMed id: 9705294  
 
 
Involvement of an active-site Zn2+ ligand in the catalytic mechanism of human glyoxalase I.
M.Ridderström, A.D.Cameron, T.A.Jones, B.Mannervik.
 
  ABSTRACT  
 
The Zn2+ ligands glutamate 99 and glutamate 172 in the active site of human glyoxalase I were replaced, each in turn, by glutamines by site-directed mutagenesis to elucidate their potential significance for the catalytic properties of the enzyme. To compensate for the loss of the charged amino acid residue, another of the metal ligands, glutamine 33, was simultaneously mutated into glutamate. The double mutants and the single mutants Q33E, E99Q, and E172Q were expressed in Escherichia coli, purified on an S-hexylglutathione matrix, and characterized. Metal analysis demonstrated that mutant Q33E/E172Q contained 1.0 mol of zinc/mol of enzyme subunit, whereas mutant Q33E/E99Q contained only 0.3 mol of zinc/mol of subunit. No catalytic activity could be detected with the double mutant Q33E/E172Q (<10(-8) of the wild-type activity). The second double mutant Q33E/E99Q had 1.5% of the specific activity of the wild-type enzyme, whereas the values for mutants Q33E and E99Q were 1.3 and 0. 1%, respectively; the E172Q mutant had less than 10(-5) times the specific activity of the wild-type. The crystal structure of the catalytically inactive double mutant Q33E/E172Q demonstrated that Zn2+ was bound without any gross changes or perturbations. The results suggest that the metal ligand glutamate 172 is directly involved in the catalytic mechanism of the enzyme, presumably serving as the base that abstracts a proton from the hemithioacetal substrate.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Overlay of the wild-type structure on the model of the Q33E/E172Q mutant. The mutant model (thin lines; crosses for the zinc and water molecules) is that obtained before the release of the noncrystallographic symmetry constraints. The wild-type structure (thick lines; solid spheres for the zinc and water molecules) has previously been published (8). The two models were superposed based on the least squares fit of their respective C atoms (residues 30-173). The glutathione derivatives bound (to the left) in the active site were S-benzylglutathione (wild-type) and S-hexylglutathione (Q33E/E172Q mutant).
Figure 3.
Fig. 3. Proposed involvement of glutamate 172 in the catalytic mechanism of glyoxalase I. A, the binding of the hemithioacetal substrate of methylglyoxal and glutathione in the active site. B, Glu-172 is released from the Zn2+, and the carboxylate group removes the C1 proton of the substrate. C, Glu-172 delivers the proton at C2. D, D-Lactoylglutathione is released and Glu-172 resumes its original Zn2+ coordination. The question marks indicate coordination to water molecules or oxygen(s) of the substrate (see Discussion).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 21623-21628) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19101977 X.Wu, P.M.Flatt, H.Xu, and T.Mahmud (2009).
Biosynthetic Gene Cluster of Cetoniacytone A, an Unusual Aminocyclitol from the Endosymbiotic Bacterium Actinomyces sp. Lu 9419.
  Chembiochem, 10, 304-314.  
15386471 M.A.Junaid, D.Kowal, M.Barua, P.S.Pullarkat, S.Sklower Brooks, and R.K.Pullarkat (2004).
Proteomic studies identified a single nucleotide polymorphism in glyoxalase I as autism susceptibility factor.
  Am J Med Genet A, 131, 11-17.  
14529289 O.Schilling, N.Wenzel, M.Naylor, A.Vogel, M.Crowder, C.Makaroff, and W.Meyer-Klaucke (2003).
Flexible metal binding of the metallo-beta-lactamase domain: glyoxalase II incorporates iron, manganese, and zinc in vivo.
  Biochemistry, 42, 11777-11786.  
11223513 M.Jaskólski, M.Kozak, J.Lubkowski, G.Palm, and A.Wlodawer (2001).
Structures of two highly homologous bacterial L-asparaginases: a case of enantiomorphic space groups.
  Acta Crystallogr D Biol Crystallogr, 57, 369-377.
PDB codes: 1hfj 1hfk 1ho3
11015195 K.V.Ramana, B.L.Dixit, S.Srivastava, G.K.Balendiran, S.K.Srivastava, and A.Bhatnagar (2000).
Selective recognition of glutathiolated aldehydes by aldose reductase.
  Biochemistry, 39, 12172-12180.  
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.