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PDBsum entry 1one

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1one
Jmol
Contents
Protein chains
436 a.a. *
Ligands
PEP-2PG ×2
Metals
_MG ×4
Waters ×942
* Residue conservation analysis
PDB id:
1one
Name: Lyase
Title: Yeast enolase complexed with an equilibrium mixture of 2'- phosphoglyceate and phosphoenolpyruvate
Structure: Enolase. Chain: a, b. Synonym: 2-phospho-d-glycerate hydrolase. Ec: 4.2.1.11
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.177    
Authors: T.M.Larsen,J.E.Wedekind,I.Rayment,G.H.Reed
Key ref:
T.M.Larsen et al. (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. PubMed id: 8605183 DOI: 10.1021/bi952859c
Date:
05-Dec-95     Release date:   11-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
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 1 residue position (black cross)

 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
Bound ligand (Het Group name = PEP)
corresponds exactly
+ 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   4 terms 
  Biological process     regulation of vacuole fusion, non-autophagic   3 terms 
  Biochemical function     protein binding     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi952859c Biochemistry 35:4349-4358 (1996)
PubMed id: 8605183  
 
 
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.
T.M.Larsen, J.E.Wedekind, I.Rayment, G.H.Reed.
 
  ABSTRACT  
 
The equilibrium mixture of yeast enolase with substrate, 2-phospho-D-glycerate (2-PGA), and product, phosphoenolpyruvate (P-enolpyruvate), has been crystallized from solutions of poly(ethylene glycol) (PEG) at pH 8.0. Crystals belong to the space group C2 and have unit cell dimensions a = 121.9 A, b = 73.2 A, c = 93.9 A, and beta = 93.3 degrees. The crystals have one dimer per asymmetric unit. Crystals of the equilibrium mixture and of the enolase complex of phosphonoacetohydroxamate (PhAH) are isomorphous, and the structure of the former complex was solved from the coordinates of enolase-(Mg2+)2-PhAH [Wedekind, J. E., Poyner, R. R., Reed, G. H., & Rayment, I. (1994) Biochemistry 33, 9333-9342]. The current crystallographic R-factor is 17.7% for all recorded data (92% complete) to 1.8 A resolution. The electron density map is unambiguous with respect to the positions and liganding of both magnesium ions and with respect to the stereochemistry of substrate/product binding. Both magnesium ions are complexed to functional groups of the substrate/product. The higher affinity Mg2+ coordinates to the carboxylate side chains of Asp 246, Glu 295, and Asp 320, both carboxylate oxygens of the substrate/product, and a water molecule. One of the carboxylate oxygens of the substrate/product also coordinates to the lower affinity Mg2+-thus forming a mu-carboxylato bridge. The other ligands of the second Mg2+ are a phosphoryl oxygen of the substrate/product, two water molecules, and the carbonyl and gamma-oxygens of Ser 39 from the active site loop. The intricate coordination of both magnesium ions to the carboxylate group suggests that both metal ions participate in stabilizing negative charge in the carbanion (aci-carboxylate) intermediate. The epsilon-amino group of Lys 345 is positioned to serve as the base in the forward reaction whereas the carboxylate side chain of Glu 211 is positioned to interact with the 3-OH of 2-PGA. The structure provides a candid view of the catalytic machinery of enolase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21249422 C.Rode, S.Gallien, D.Heintz, A.Van Dorsselaer, H.P.Braun, and T.Winkelmann (2011).
Enolases: storage compounds in seeds? Evidence from a proteomic comparison of zygotic and somatic embryos of Cyclamen persicum Mill.
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19924403 D.S.Sánchez-Miguel, J.Romero-Jiménez, C.A.Reyes-López, A.L.Cabrera-Avila, N.Carrillo-Ibarra, and C.G.Benítez-Cardoza (2010).
Chemical unfolding of enolase from Saccharomyces cerevisiae exhibits a three-state model.
  Protein J, 29, 1.  
19883118 J.F.Rakus, C.Kalyanaraman, A.A.Fedorov, E.V.Fedorov, F.P.Mills-Groninger, R.Toro, J.Bonanno, K.Bain, J.M.Sauder, S.K.Burley, S.C.Almo, M.P.Jacobson, and J.A.Gerlt (2009).
Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .
  Biochemistry, 48, 11546-11558.
PDB codes: 2oqy 3es7 3es8 3fyy 3hpf
  19255486 J.Wang, Y.F.Zhou, L.F.Li, and X.D.Su (2009).
Crystallization and preliminary X-ray analysis of human liver alpha-enolase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 288-290.  
18560153 H.J.Kang, S.K.Jung, S.J.Kim, and S.J.Chung (2008).
Structure of human alpha-enolase (hENO1), a multifunctional glycolytic enzyme.
  Acta Crystallogr D Biol Crystallogr, 64, 651-657.
PDB code: 3b97
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
17367133 R.Carmieli, T.M.Larsen, G.H.Reed, S.Zein, F.Neese, and D.Goldfarb (2007).
The catalytic Mn2+ sites in the enolase-inhibitor complex: crystallography, single-crystal EPR, and DFT calculations.
  J Am Chem Soc, 129, 4240-4252.  
16411755 J.Qin, G.Chai, J.M.Brewer, L.L.Lovelace, and L.Lebioda (2006).
Fluoride inhibition of enolase: crystal structure and thermodynamics.
  Biochemistry, 45, 793-800.
PDB codes: 2akm 2akz
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
12952952 E.L.Wise, D.E.Graham, R.H.White, and I.Rayment (2003).
The structural determination of phosphosulfolactate synthase from Methanococcus jannaschii at 1.7-A resolution: an enolase that is not an enolase.
  J Biol Chem, 278, 45858-45863.
PDB code: 1qwg
14579358 R.C.Rittenhouse, W.K.Apostoluk, J.H.Miller, and T.P.Straatsma (2003).
Characterization of the active site of DNA polymerase beta by molecular dynamics and quantum chemical calculation.
  Proteins, 53, 667-682.  
12084062 J.Mima, G.Jung, T.Onizuka, H.Ueno, and R.Hayashi (2002).
Amphipathic property of free thiol group contributes to an increase in the catalytic efficiency of carboxypeptidase Y.
  Eur J Biochem, 269, 3220-3225.  
12084063 L.F.García-Alles, and B.Erni (2002).
Synthesis of phosphoenol pyruvate (PEP) analogues and evaluation as inhibitors of PEP-utilizing enzymes.
  Eur J Biochem, 269, 3226-3236.  
11741915 L.F.Garcia-Alles, K.Flükiger, J.Hewel, R.Gutknecht, C.Siebold, S.Schürch, and B.Erni (2002).
Mechanism-based inhibition of enzyme I of the Escherichia coli phosphotransferase system. Cysteine 502 is an essential residue.
  J Biol Chem, 277, 6934-6942.  
11748244 M.Asuncion, W.Blankenfeldt, J.N.Barlow, D.Gani, and J.H.Naismith (2002).
The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step.
  J Biol Chem, 277, 8306-8311.
PDB codes: 1kcz 1kd0
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11738171 J.P.Richard, and T.L.Amyes (2001).
Proton transfer at carbon.
  Curr Opin Chem Biol, 5, 626-633.  
11526220 P.J.Keeling, and J.D.Palmer (2001).
Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase.
  Proc Natl Acad Sci U S A, 98, 10745-10750.  
11371198 R.A.Farley, E.Elquza, J.Müller-Ehmsen, D.J.Kane, A.K.Nagy, V.N.Kasho, and L.D.Faller (2001).
18O-exchange evidence that mutations of arginine in a signature sequence for P-type pumps affect inorganic phosphate binding.
  Biochemistry, 40, 6361-6370.  
11093265 W.S.Valdar, and J.M.Thornton (2001).
Protein-protein interfaces: analysis of amino acid conservation in homodimers.
  Proteins, 42, 108-124.  
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
11058743 D.R.Flower, A.C.North, and C.E.Sansom (2000).
The lipocalin protein family: structural and sequence overview.
  Biochim Biophys Acta, 1482, 9.  
11106410 S.Wagner, H.Breiteneder, B.Simon-Nobbe, M.Susani, M.Krebitz, B.Niggemann, R.Brehler, O.Scheiner, and K.Hoffmann-Sommergruber (2000).
Hev b 9, an enolase and a new cross-reactive allergen from hevea latex and molds. Purification, characterization, cloning and expression.
  Eur J Biochem, 267, 7006-7014.  
10978150 T.B.Thompson, J.B.Garrett, E.A.Taylor, R.Meganathan, J.A.Gerlt, and I.Rayment (2000).
Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate.
  Biochemistry, 39, 10662-10676.
PDB codes: 1fhu 1fhv
10194342 D.R.Palmer, J.B.Garrett, V.Sharma, R.Meganathan, P.C.Babbitt, and J.A.Gerlt (1999).
Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase.
  Biochemistry, 38, 4252-4258.  
10600135 E.L.Hegg, A.K.Whiting, R.E.Saari, J.McCracken, R.P.Hausinger, and L.Que (1999).
Herbicide-degrading alpha-keto acid-dependent enzyme TfdA: metal coordination environment and mechanistic insights.
  Biochemistry, 38, 16714-16726.  
10425687 I.A.Shumilin, R.H.Kretsinger, and R.H.Bauerle (1999).
Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli.
  Structure, 7, 865-875.
PDB code: 1qr7
10378273 K.Huang, Z.Li, Y.Jia, D.Dunaway-Mariano, and O.Herzberg (1999).
Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate.
  Structure, 7, 539-548.
PDB code: 1pym
9772161 A.M.Gulick, D.R.Palmer, P.C.Babbitt, J.A.Gerlt, and I.Rayment (1998).
Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.
  Biochemistry, 37, 14358-14368.
PDB code: 1bqg
9790688 D.A.Vinarov, and T.Nowak (1998).
pH dependence of the reaction catalyzed by yeast Mg-enolase.
  Biochemistry, 37, 15238-15246.  
9772160 D.R.Palmer, B.K.Hubbard, and J.A.Gerlt (1998).
Evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida.
  Biochemistry, 37, 14350-14357.  
9724714 M.S.Hasson, I.Schlichting, J.Moulai, K.Taylor, W.Barrett, G.L.Kenyon, P.C.Babbitt, J.A.Gerlt, G.A.Petsko, and D.Ringe (1998).
Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase.
  Proc Natl Acad Sci U S A, 95, 10396-10401.
PDB code: 1bkh
9748211 W.W.Cleland, P.A.Frey, and J.A.Gerlt (1998).
The low barrier hydrogen bond in enzymatic catalysis.
  J Biol Chem, 273, 25529-25532.  
9348662 C.L.Perrin, and J.B.Nielson (1997).
"Strong" hydrogen bonds in chemistry and biology.
  Annu Rev Phys Chem, 48, 511-544.  
9254698 T.Hermann, P.Auffinger, W.G.Scott, and E.Westhof (1997).
Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.
  Nucleic Acids Res, 25, 3421-3427.  
9201952 V.N.Kasho, M.Stengelin, I.N.Smirnova, and L.D.Faller (1997).
A proposal for the Mg2+ binding site of P-type ion motive ATPases and the mechanism of phosphoryl group transfer.
  Biochemistry, 36, 8045-8052.  
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.  
9000033 J.Stubbe, and L.N.Johnson (1996).
Catalysis and regulation.
  Curr Opin Struct Biol, 6, 733-735.  
8987982 P.C.Babbitt, M.S.Hasson, J.E.Wedekind, D.R.Palmer, W.C.Barrett, G.H.Reed, I.Rayment, D.Ringe, G.L.Kenyon, and J.A.Gerlt (1996).
The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
  Biochemistry, 35, 16489-16501.  
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.