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PDBsum entry 3enl

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Carbon-oxygen lyase PDB id
3enl
Jmol
Contents
Protein chain
436 a.a. *
Ligands
SO4
Waters ×353
* Residue conservation analysis
PDB id:
3enl
Name: Carbon-oxygen lyase
Title: Refined structure of yeast apo-enolase at 2.25 angstroms resolution
Structure: Enolase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
Resolution:
2.25Å     R-factor:   0.154    
Authors: L.Lebioda,B.Stec
Key ref: B.Stec and L.Lebioda (1990). Refined structure of yeast apo-enolase at 2.25 A resolution. J Mol Biol, 211, 235-248. PubMed id: 2405163 DOI: 10.1016/0022-2836(90)90023-F
Date:
13-Nov-90     Release date:   15-Apr-92    
Supersedes: 2enl
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
= 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: 10.1016/0022-2836(90)90023-F J Mol Biol 211:235-248 (1990)
PubMed id: 2405163  
 
 
Refined structure of yeast apo-enolase at 2.25 A resolution.
B.Stec, L.Lebioda.
 
  ABSTRACT  
 
The crystal structure of apo-enolase from baker's yeast (Saccharomyces cerevisiae) was established at 2.25 A resolution using a restrained least-squares refinement method. Based on 21,077 independent reflections of better than 8 A resolution, a final R-factor of 15.4% was obtained with a model obeying standard geometry within 0.017 A in bond length and 3.5 degrees in bond angles. The upper limit for the co-ordinate accuracy of the atoms was estimated to be 0.18 A. The refinement confirmed the heterodox, non-parallel character of the 8-fold beta alpha-barrel domain with beta beta alpha alpha(beta alpha)6 topology. The reported structure for which the data were collected at pH 5.0 represents an apo-form of the enzyme. Of the three carboxylic ligands that form the conformational metal ion binding site two, Glu295 and Asp320, are very close and presumably form a strong acidic type hydrogen bond with the proton partially replacing the electric charge of the physiological cofactor Mg2+. The single sulfate ion found in the structure is in the active site cavity, co-ordinated to the side-chains of Lys345 and Arg374, and to the N atom of Ser375. It is located about 7.4 A from the conformational metal ion binding site. It occupies the site in which the phosphate group of the substrate binds.
 

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.  
  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.  
17434746 C.S.Kaddis, S.H.Lomeli, S.Yin, B.Berhane, M.I.Apostol, V.A.Kickhoefer, L.H.Rome, and J.A.Loo (2007).
Sizing large proteins and protein complexes by electrospray ionization mass spectrometry and ion mobility.
  J Am Soc Mass Spectrom, 18, 1206-1216.  
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.  
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.  
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.  
10823940 D.M.van Aalten, B.Synstad, M.B.Brurberg, E.Hough, B.W.Riise, V.G.Eijsink, and R.K.Wierenga (2000).
Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-A resolution.
  Proc Natl Acad Sci U S A, 97, 5842-5847.
PDB code: 1e15
10734095 S.Radaev, P.Dastidar, M.Patel, R.W.Woodard, and D.L.Gatti (2000).
Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.
  J Biol Chem, 275, 9476-9484.
PDB code: 1d9e
  9457431 J.P.Martínez, M.L.Gil, J.L.López-Ribot, and W.L.Chaffin (1998).
Serologic response to cell wall mannoproteins and proteins of Candida albicans.
  Clin Microbiol Rev, 11, 121-141.  
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.  
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.  
  7757011 H.Schurig, K.Rutkat, R.Rachel, and R.Jaenicke (1995).
Octameric enolase from the hyperthermophilic bacterium Thermotoga maritima: purification, characterization, and image processing.
  Protein Sci, 4, 228-236.  
7544233 K.Ito, A.Ishiguro, T.Kanbe, K.Tanaka, and S.Torii (1995).
Characterization of IgE-binding epitopes on Candida albicans enolase.
  Clin Exp Allergy, 25, 529-535.  
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.  
8592705 T.Sandalova, and Y.Lindqvist (1995).
Three-dimensional model of the alpha-subunit of bacterial luciferase.
  Proteins, 23, 241-255.  
8159666 C.W.van Gelder, F.J.Leusen, J.A.Leunissen, and J.H.Noordik (1994).
A molecular dynamics approach for the generation of complete protein structures from limited coordinate data.
  Proteins, 18, 174-185.  
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.  
  8478328 A.B.Mason, H.R.Buckley, and J.A.Gorman (1993).
Molecular cloning and characterization of the Candida albicans enolase gene.
  J Bacteriol, 175, 2632-2639.  
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
  1400228 P.Sundstrom, and G.R.Aliaga (1992).
Molecular cloning of cDNA and analysis of protein secondary structure of Candida albicans enolase, an abundant, immunodominant glycolytic enzyme.
  J Bacteriol, 174, 6789-6799.  
2275753 C.C.Chin (1990).
The primary structure of rabbit muscle enolase.
  J Protein Chem, 9, 427-432.  
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.