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PDBsum entry 1pdy

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Lyase (carbon-oxygen) PDB id
1pdy
Jmol
Contents
Protein chain
434 a.a. *
Ligands
SO4
Waters ×112
* Residue conservation analysis
PDB id:
1pdy
Name: Lyase (carbon-oxygen)
Title: X-ray structure and catalytic mechanism of lobster enolase
Structure: Enolase. Chain: a. Synonym: 2-phospho-d-glycerate dehydratase. Ec: 4.2.1.11
Source: Homarus gammarus. European lobster. Organism_taxid: 6707. Organ: tail. Tissue: tail muscle
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.215    
Authors: J.Janin,S.Duquerroy,C.Camus,G.Le Bras
Key ref:
S.Duquerroy et al. (1995). X-ray structure and catalytic mechanism of lobster enolase. Biochemistry, 34, 12513-12523. PubMed id: 7547999 DOI: 10.1021/bi00039a005
Date:
05-Jun-95     Release date:   14-Nov-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56252  (ENO_HOMGA) -  Enolase
Seq:
Struc:
433 a.a.
433 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.11  - Phosphopyruvate hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O
2-phospho-D-glycerate
= phosphoenolpyruvate
+ H(2)O
      Cofactor: Mg(2+)
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     glycolysis   1 term 
  Biochemical function     lyase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi00039a005 Biochemistry 34:12513-12523 (1995)
PubMed id: 7547999  
 
 
X-ray structure and catalytic mechanism of lobster enolase.
S.Duquerroy, C.Camus, J.Janin.
 
  ABSTRACT  
 
Enolase prepared from lobster tail muscle yielded trigonal crystals with one 47 kDa subunit per asymmetric unit. X-ray data were collected on the apoenzyme at 2.4 A resolution and on a complex with Mn2+ and the inhibitor phosphoglycolate at 2.2 A resolution. The corresponding cDNA was amplified from a library of lobster muscle cDNA, and a sequence corresponding to residues 27-398 was determined. It is highly homologous to other enolases, including yeast enolase for which an X-ray structure is available. Yeast enolase was used as a starting point for crystallographic refinement, which led to models of lobster enolase having R-factors below 22% and good stereochemistry. These models are very similar to yeast enolase; they have the same fold with a beta 3 alpha 4 N-terminal domain followed by an atypical alpha/beta barrel. Lobster apoenolase and the ternary complex differ only in the position of three mobile loops. In the complex, a single Mn2+ ion is seen ligated to three carboxylates and three water molecules. Phosphoglycolate binds near, but not directly to, the metal. His 157, which belongs to one of the mobile loops, is in contact with the C2 atom of the ligand. A water molecule hydrogen-bonds to the carboxylate of the ligand and to those of Glu 166 and Glu 209. We suggest that His 157 is the base that abstracts the C2H proton, whereas the water molecule is part of a proton relay system keeping the substrate in the carboxylic acid form where the pKa of the C2H group is low enough for proton transfer to His 157. The resulting catalytic mechanism is different from those proposed on the basis of the yeast enzyme X-ray structures, but it fits with earlier biochemical and spectroscopic data.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20098674 F.Karbassi, V.Quiros, V.Pancholi, and M.J.Kornblatt (2010).
Dissociation of the octameric enolase from S. pyogenes--one interface stabilizes another.
  PLoS One, 5, e8810.  
19455663 E.Menkhorst, L.Selwood, and S.Cui (2009).
Uterine expression of cp4 gene homolog in the Stripe-faced Dunnart, Sminthopsis macroura: relationship with conceptus development and progesterone profile.
  Mol Reprod Dev, 76, 863-872.  
  18997349 H.Yamamoto, and N.Kunishima (2008).
Purification, crystallization and preliminary crystallographic study of the putative enolase MJ0232 from the hyperthermophilic archaeon Methanococcus jannaschii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1087-1090.  
17371507 I.Pal-Bhowmick, S.Krishnan, and G.K.Jarori (2007).
Differential susceptibility of Plasmodium falciparum versus yeast and mammalian enolases to dissociation into active monomers.
  FEBS J, 274, 1932-1945.  
15508143 R.Sankararamakrishnan, S.Verma, and S.Kumar (2005).
ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis.
  Proteins, 58, 211-221.  
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
15373835 M.J.Kornblatt, R.Lange, and C.Balny (2004).
Use of hydrostatic pressure to produce 'native' monomers of yeast enolase.
  Eur J Biochem, 271, 3897-3904.  
12527789 C.Blouin, Y.Boucher, and A.J.Roger (2003).
Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.
  Nucleic Acids Res, 31, 790-797.  
12704724 S.Cui, and L.Selwood (2003).
Cloning and expression of a novel cDNA encoding shell coat protein, cp4, from the brushtail possum (Trichosurus vulpecula).
  Mol Reprod Dev, 65, 141-147.  
12869196 V.Hannaert, M.A.Albert, D.J.Rigden, M.T.da Silva Giotto, O.Thiemann, R.C.Garratt, J.Van Roy, F.R.Opperdoes, and P.A.Michels (2003).
Kinetic characterization, structure modelling studies and crystallization of Trypanosoma brucei enolase.
  Eur J Biochem, 270, 3205-3213.  
11512153 C.L.Verlinde, V.Hannaert, C.Blonski, M.Willson, J.J.Périé, L.A.Fothergill-Gilmore, F.R.Opperdoes, M.H.Gelb, W.G.Hol, and P.A.Michels (2001).
Glycolysis as a target for the design of new anti-trypanosome drugs.
  Drug Resist Updat, 4, 50-65.  
11506403 G.P.Comi, F.Fortunato, S.Lucchiari, A.Bordoni, A.Prelle, S.Jann, A.Keller, P.Ciscato, S.Galbiati, L.Chiveri, Y.Torrente, G.Scarlato, and N.Bresolin (2001).
Beta-enolase deficiency, a new metabolic myopathy of distal glycolysis.
  Ann Neurol, 50, 202-207.  
  10211836 D.R.Westhead, T.W.Slidel, T.P.Flores, and J.M.Thornton (1999).
Protein structural topology: Automated analysis and diagrammatic representation.
  Protein Sci, 8, 897-904.  
10535916 S.Shan, A.Yoshida, S.Sun, J.A.Piccirilli, and D.Herschlag (1999).
Three metal ions at the active site of the Tetrahymena group I ribozyme.
  Proc Natl Acad Sci U S A, 96, 12299-12304.  
9790688 D.A.Vinarov, and T.Nowak (1998).
pH dependence of the reaction catalyzed by yeast Mg-enolase.
  Biochemistry, 37, 15238-15246.  
8994873 G.H.Reed, R.R.Poyner, T.M.Larsen, J.E.Wedekind, and I.Rayment (1996).
Structural and mechanistic studies of enolase.
  Curr Opin Struct Biol, 6, 736-743.  
8634301 R.R.Poyner, L.T.Laughlin, G.A.Sowa, and G.H.Reed (1996).
Toward identification of acid/base catalysts in the active site of enolase: comparison of the properties of K345A, E168Q, and E211Q variants.
  Biochemistry, 35, 1692-1699.  
8605183 T.M.Larsen, J.E.Wedekind, I.Rayment, and G.H.Reed (1996).
A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution.
  Biochemistry, 35, 4349-4358.
PDB code: 1one
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.