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PDBsum entry 7enl

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protein ligands metals links
Carbon-oxygen lyase PDB id
7enl
Jmol
Contents
Protein chain
436 a.a. *
Ligands
2PG
Metals
_MG
Waters ×347
* Residue conservation analysis
PDB id:
7enl
Name: Carbon-oxygen lyase
Title: Mechanism of enolase: the crystal structure of enolase-mg2+- phosphoglycerate(slash) phosphoenolpyruvate complex at 2.2- resolution
Structure: Enolase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.169    
Authors: L.Lebioda,B.Stec
Key ref:
L.Lebioda and B.Stec (1991). Mechanism of enolase: the crystal structure of enolase-Mg2(+)-2-phosphoglycerate/phosphoenolpyruvate complex at 2.2-A resolution. Biochemistry, 30, 2817-2822. PubMed id: 2007120 DOI: 10.1021/bi00225a012
Date:
13-Nov-90     Release date:   15-Apr-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00924  (ENO1_YEAST) -  Enolase 1
Seq:
Struc:
437 a.a.
436 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.4.2.1.11  - Phosphopyruvate hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O
2-phospho-D-glycerate
Bound ligand (Het Group name = 2PG)
corresponds exactly
= phosphoenolpyruvate
+ H(2)O
      Cofactor: Magnesium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   4 terms 
  Biological process     regulation of vacuole fusion, non-autophagic   3 terms 
  Biochemical function     protein binding     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi00225a012 Biochemistry 30:2817-2822 (1991)
PubMed id: 2007120  
 
 
Mechanism of enolase: the crystal structure of enolase-Mg2(+)-2-phosphoglycerate/phosphoenolpyruvate complex at 2.2-A resolution.
L.Lebioda, B.Stec.
 
  ABSTRACT  
 
Enolase in the presence of Mg2+ catalyzes the elimination of H2O from 2-phosphoglyceric acid (PGA) to form phosphoenolpyruvate (PEP) and the reverse reaction, the hydration of PEP to PGA. The structure of the ternary complex yeast enolase-Mg2(+)-PGA/PEP has been determined by X-ray diffraction and refined by crystallographic restrained least-squares to an R = 16.9% for those data with I/sigma (I) greater than or equal to 2 to 2.2-A resolution with a good geometry of the model. The structure indicates the substrate molecule in the active site has its hydroxyl group coordinated to the Mg2+ ion. The carboxylic group interacts with the side chains of His373 and Lys396. The phosphate group is H-bonded to the guanidinium group of Arg374. A water molecule H-bonded to the carboxylic groups of Glu168 and Glu211 is located at a 2.6-A distance from carbon-2 of the substrate in the direction of its proton. We propose that this cluster functions as the base abstracting the proton in the catalytic process. The proton is probably transferred, first to the water molecule, then to Glu168, and further to the substrate hydroxyl to form a water molecule. Some analogy is apparent between the initial stages of the enolase reverse reaction, the hydration of PEP, and the proteolytic mechanism of the metallohydrolases carboxypeptidase A and thermolysin. The substrate/product binding is accompanied by large movements of loops Ser36-His43 and Ser158-Gly162. The role of these conformational changes is not clear at this time.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17822439 M.V.de A S Navarro, S.M.Gomes Dias, L.V.Mello, M.T.da Silva Giotto, S.Gavalda, C.Blonski, R.C.Garratt, and D.J.Rigden (2007).
Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics.
  FEBS J, 274, 5077-5089.
PDB codes: 2ptw 2ptx 2pty 2ptz 2pu0 2pu1
16049725 E.Rodríguez, F.Romarís, S.Lorenzo, J.Moreno, P.Bonay, F.M.Ubeira, and T.Gárate (2006).
A recombinant enolase from Anisakis simplex is differentially recognized in natural human and mouse experimental infections.
  Med Microbiol Immunol, 195, 1.  
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
14760744 K.Gunasekaran, and R.Nussinov (2004).
Modulating functional loop movements: the role of highly conserved residues in the correlated loop motions.
  Chembiochem, 5, 224-230.  
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.  
10769114 A.M.Gulick, B.K.Hubbard, J.A.Gerlt, and I.Rayment (2000).
Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.
  Biochemistry, 39, 4590-4602.
PDB codes: 1ec7 1ec8 1ec9 1ecq
11114510 H.Erlandsen, E.E.Abola, and R.C.Stevens (2000).
Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites.
  Curr Opin Struct Biol, 10, 719-730.  
9790688 D.A.Vinarov, and T.Nowak (1998).
pH dependence of the reaction catalyzed by yeast Mg-enolase.
  Biochemistry, 37, 15238-15246.  
9799503 W.A.King, J.E.Gready, and T.J.Andrews (1998).
Quantum chemical analysis of the enolization of ribulose bisphosphate: the first hurdle in the fixation of CO2 by Rubisco.
  Biochemistry, 37, 15414-15422.  
8662913 C.H.Bu, and T.Pourmotabbed (1996).
Mechanism of Ca2+-dependent activity of human neutrophil gelatinase B.
  J Biol Chem, 271, 14308-14315.  
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.  
8617289 M.J.Kornblatt, A.Al-Ghanim, and J.A.Kornblatt (1996).
The effects of sodium perchlorate on rabbit muscle enolase--Spectral characterization of the monomer.
  Eur J Biochem, 236, 78-84.  
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
7648455 B.A.Baldo (1995).
Allergenic crossreactivity of fungi with emphasis on yeasts: strategies for further study.
  Clin Exp Allergy, 25, 488-492.  
7784428 D.W.Deerfield, D.J.Fox, M.Head-Gordon, R.G.Hiskey, and L.G.Pedersen (1995).
The first solvation shell of magnesium ion in a model protein environment with formate, water, and X-NH3, H2S, imidazole, formaldehyde, and chloride as ligands: an Ab initio study.
  Proteins, 21, 244-255.  
7648459 K.Ito, A.Ishiguro, T.Kanbe, K.Tanaka, and S.Torii (1995).
Detection of IgE antibody against Candida albicans enolase and its crossreactivity to Saccharomyces cerevisiae enolase.
  Clin Exp Allergy, 25, 522-528.  
7735837 X.Wu, B.Knudsen, S.M.Feller, J.Zheng, A.Sali, D.Cowburn, H.Hanafusa, and J.Kuriyan (1995).
Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk.
  Structure, 3, 215-226.
PDB codes: 1cka 1ckb
  8003972 C.L.Borders, J.A.Broadwater, P.A.Bekeny, J.E.Salmon, A.S.Lee, A.M.Eldridge, and V.B.Pett (1994).
A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens.
  Protein Sci, 3, 541-548.  
8125109 M.Read, K.E.Hicks, P.F.Sims, and J.E.Hyde (1994).
Molecular characterisation of the enolase gene from the human malaria parasite Plasmodium falciparum. Evidence for ancestry within a photosynthetic lineage.
  Eur J Biochem, 220, 513-520.  
8108383 J.M.Brewer, R.L.Robson, C.V.Glover, M.J.Holland, and L.Lebioda (1993).
Preparation and characterization of the E168Q site-directed mutant of yeast enolase 1.
  Proteins, 17, 426-434.  
8346189 L.Lebioda, E.Zhang, K.Lewinski, and J.M.Brewer (1993).
Fluoride inhibition of yeast enolase: crystal structure of the enolase-Mg(2+)-F(-)-Pi complex at 2.6 A resolution.
  Proteins, 16, 219-225.
PDB code: 1nel
  8514750 R.B.Bourret, S.K.Drake, S.A.Chervitz, M.I.Simon, and J.J.Falke (1993).
Activation of the phosphosignaling protein CheY. II. Analysis of activated mutants by 19F NMR and protein engineering.
  J Biol Chem, 268, 13089-13096.  
  8514749 S.K.Drake, R.B.Bourret, L.A.Luck, M.I.Simon, and J.J.Falke (1993).
Activation of the phosphosignaling protein CheY. I. Analysis of the phosphorylated conformation by 19F NMR and protein engineering.
  J Biol Chem, 268, 13081-13088.  
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.