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PDBsum entry 1ebh

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protein metals Protein-protein interface(s) links
Carbon-oxygen lyase PDB id
1ebh
Jmol
Contents
Protein chains
436 a.a. *
Metals
_MG ×2
_CL ×2
Waters ×507
* Residue conservation analysis
PDB id:
1ebh
Name: Carbon-oxygen lyase
Title: Octahedral coordination at the high affinity metal site in enolase; crystallographic analysis of the mg++-enzyme from yeast at 1.9 angstroms resolution
Structure: Enolase. Chain: a, b. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.190    
Authors: J.E.Wedekind,G.H.Reed,I.Rayment
Key ref:
J.E.Wedekind et al. (1995). Octahedral coordination at the high-affinity metal site in enolase: crystallographic analysis of the MgII--enzyme complex from yeast at 1.9 A resolution. Biochemistry, 34, 4325-4330. PubMed id: 7703246 DOI: 10.1021/bi00013a022
Date:
01-Nov-94     Release date:   27-Apr-95    
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
= 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   4 terms 
  Biological process     regulation of vacuole fusion, non-autophagic   3 terms 
  Biochemical function     protein binding     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi00013a022 Biochemistry 34:4325-4330 (1995)
PubMed id: 7703246  
 
 
Octahedral coordination at the high-affinity metal site in enolase: crystallographic analysis of the MgII--enzyme complex from yeast at 1.9 A resolution.
J.E.Wedekind, G.H.Reed, I.Rayment.
 
  ABSTRACT  
 
The structure of the Mg2+ complex of yeast enolase has been determined from crystals grown in solutions of poly(ethylene glycol) at pH 8.1. Crystals belong to the space group P2(1) and have unit cell dimensions a = 72.5 A, b = 73.2 A, c = 89.1 A, and beta = 104.4 degrees. There is one dimer in the asymmetric unit. The current crystallographic R-factor is 19.0% for all recorded data to 1.9 A resolution. The electron density indicates a hexacoordinate Mg2+ at the high-affinity cation binding site. The octahedral coordination sphere consists of a meridional arrangement of three carboxylate oxygens from the side chains of Asp 246, Asp 320, and Glu 295, and three well-ordered water molecules. Octahedral coordination is the preferred geometry for alkaline earth metal ions in complexes with oxygen donor groups. In previous crystallographic studies of enolase, Zn2+ and Mg2+ complexes at the high-affinity site were reported to exist in trigonal bipyramidal coordination. This geometry was suggested to enhance the electrophilicity of the metal ion and promote rapid ligand exchange [Lebioda, L., & Stec, B. (1989) J. Am. Chem. Soc. 111, 8511-8513]. The octahedral arrangement of carboxylate and water ligands in the MgII-enolase complex determined here is most consistent with reports of the Mn2+ and Mg2+ coordination complexes of mandelate racemase and muconate lactonizing enzyme. These latter enzymes have alpha/beta-barrel folds comparable to enolase.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
12393860 C.V.Smith, C.C.Huang, A.Miczak, D.G.Russell, J.C.Sacchettini, and K.Höner zu Bentrup (2003).
Biochemical and structural studies of malate synthase from Mycobacterium tuberculosis.
  J Biol Chem, 278, 1735-1743.
PDB codes: 1n8i 1n8w
12577262 J.B.Mitchell, and J.Smith (2003).
D-amino acid residues in peptides and proteins.
  Proteins, 50, 563-571.  
14579361 R.P.Bahadur, P.Chakrabarti, F.Rodier, and J.Janin (2003).
Dissecting subunit interfaces in homodimeric proteins.
  Proteins, 53, 708-719.  
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.  
11738171 J.P.Richard, and T.L.Amyes (2001).
Proton transfer at carbon.
  Curr Opin Chem Biol, 5, 626-633.  
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
9818186 J.A.Gerlt, and P.C.Babbitt (1998).
Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis.
  Curr Opin Chem Biol, 2, 607-612.  
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
9388188 P.C.Babbitt, and J.A.Gerlt (1997).
Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities.
  J Biol Chem, 272, 30591-30594.  
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.  
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.  
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.