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PDBsum entry 2one

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
2one
Jmol
Contents
Protein chains
436 a.a. *
Ligands
2PG
PEP
Metals
_MG ×2
_LI
Waters ×356
* Residue conservation analysis
PDB id:
2one
Name: Lyase
Title: Asymmetric yeast enolase dimer complexed with resolved 2'- phosphoglycerate 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: Homo-Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.137    
Authors: L.Lebioda
Key ref:
E.Zhang et al. (1997). Mechanism of enolase: the crystal structure of asymmetric dimer enolase-2-phospho-D-glycerate/enolase-phosphoenolpyruvate at 2.0 A resolution. Biochemistry, 36, 12526-12534. PubMed id: 9376357 DOI: 10.1021/bi9712450
Date:
08-Sep-97     Release date:   14-Jan-98    
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
+ 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/bi9712450 Biochemistry 36:12526-12534 (1997)
PubMed id: 9376357  
 
 
Mechanism of enolase: the crystal structure of asymmetric dimer enolase-2-phospho-D-glycerate/enolase-phosphoenolpyruvate at 2.0 A resolution.
E.Zhang, J.M.Brewer, W.Minor, L.A.Carreira, L.Lebioda.
 
  ABSTRACT  
 
Enolase, a glycolytic enzyme that catalyzes the dehydration of 2-phospho-d-glycerate (PGA) to form phosphoenolpyruvate (PEP), is a homodimer in all eukaryotes and many prokaryotes. Here, we report the crystal structure of a complex between yeast enolase and an equilibrium mixture of PGA and PEP. The structure has been refined using 29 854 reflections with an F/sigma(F) of >/=3 to an R of 0.137 with average deviations of bond lengths and bond angles from ideal values of 0.013 A and 3.1 degrees , respectively. In this structure, the dimer constitutes the crystallographic asymmetric unit. The two subunits are similar, and their superposition gives a rms distance between Calpha atoms of 0.91 A. The exceptions to this are the catalytic loop Val153-Phe169 where the atomic positions in the two subunits differ by up to 4 A and the loop Ser250-Gln277, which follows the catalytic loop Val153-Phe169. In the first subunit, the imidazole side chain of His159 is in contact with the phosphate group of the substrate/product molecule; in the other it is separated by water molecules. A series of hydrogen bonds leading to a neighboring enolase dimer can be identified as being responsible for ordering and stabilization of the conformationally different subunits in the crystal lattice. The electron density present in the active site suggests that in the active site with the direct ligand-His159 hydrogen bond PGA is predominantly bound while in the active site where water molecules separate His159 from the ligand the binding of PEP dominates. The structure indicates that the water molecule hydrating carbon-3 of PEP in the PEP --> PGA reaction is activated by the carboxylates of Glu168 and Glu211. The crystals are unique because they have resolved two intermediates on the opposite sides of the transition state.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20923858 Y.Liu, Y.Li, H.Wang, R.Xia, X.Li, H.Wan, L.Qin, D.Jiang, C.Lu, and Z.Xiang (2010).
cDNA cloning and expression pattern of two enolase genes from the Chinese oak silkworm, Antheraea pernyi.
  Acta Biochim Biophys Sin (Shanghai), 42, 816-826.  
  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
18366394 J.C.Chung, M.J.Oh, S.H.Choi, and C.D.Bae (2008).
Proteomic analysis to identify biomarker proteins in pancreatic ductal adenocarcinoma.
  ANZ J Surg, 78, 245-251.  
18070902 V.Mundodi, A.S.Kucknoor, and J.F.Alderete (2008).
Immunogenic and plasminogen-binding surface-associated alpha-enolase of Trichomonas vaginalis.
  Infect Immun, 76, 523-531.  
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.  
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
16615856 D.Hakobyan, and K.Nazaryan (2006).
Molecular dynamics simulation of interactions in glycolytic enzymes.
  Biochemistry (Mosc), 71, 370-375.  
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
16287166 D.Agudo, D.Agudo Garcillán, F.Gómez-Esquer, G.Díaz-Gil, F.Martínez-Arribas, J.Delcán, J.Schneider, M.A.Palomar, and R.Linares (2005).
Proteomic analysis of the Gallus gallus embryo at stage-29 of development.
  Proteomics, 5, 4946-4957.  
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.  
14709840 S.Tanaka, K.I.Tatsumi, T.Takano, Y.Murakami, T.Takao, N.Yamakita, S.Tahara, A.Teramoto, K.Hashimoto, Y.Kato, and N.Amino (2003).
Anti-alpha-enolase antibodies in pituitary disease.
  Endocr J, 50, 697-702.  
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.  
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.  
11093265 W.S.Valdar, and J.M.Thornton (2001).
Protein-protein interfaces: analysis of amino acid conservation in homodimers.
  Proteins, 42, 108-124.  
  10850800 K.M.Holtz, B.Stec, J.K.Myers, S.M.Antonelli, T.S.Widlanski, and E.R.Kantrowitz (2000).
Alternate modes of binding in two crystal structures of alkaline phosphatase-inhibitor complexes.
  Protein Sci, 9, 907-915.
PDB codes: 1ew8 1ew9
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.  
10535937 E.M.Khalil, J.De Angelis, M.Ishii, and P.A.Cole (1999).
Mechanism-based inhibition of the melatonin rhythm enzyme: pharmacologic exploitation of active site functional plasticity.
  Proc Natl Acad Sci U S A, 96, 12418-12423.  
10455162 F.Dzierszinski, O.Popescu, C.Toursel, C.Slomianny, B.Yahiaoui, and S.Tomavo (1999).
The protozoan parasite Toxoplasma gondii expresses two functional plant-like glycolytic enzymes. Implications for evolutionary origin of apicomplexans.
  J Biol Chem, 274, 24888-24895.  
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
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.