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PDBsum entry 1oep

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protein ligands metals links
Lyase PDB id
1oep
Jmol
Contents
Protein chain
422 a.a. *
Ligands
SO4
EDO ×3
Metals
_ZN ×2
Waters ×239
* Residue conservation analysis
PDB id:
1oep
Name: Lyase
Title: Structure of trypanosoma brucei enolase reveals the inhibitory divalent metal site
Structure: Enolase. Chain: a. Synonym: 2-phosphoglycerate dehydratase, 2-phospho-d- glycerate hydro-lyase. Engineered: yes. Other_details: chain a has covalently linked 2 visible residues in an artefactual n-terminal extension resulting from cleavage of his-tag, residues -3 to -1
Source: Trypanosoma brucei brucei. Organism_taxid: 5702. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.3Å     R-factor:   0.210     R-free:   0.251
Authors: M.T.Da Silva Giotto,M.V.A.S.Navarro,R.C.Garratt,D.J.Rigden
Key ref:
M.T.da Silva Giotto et al. (2003). The crystal structure of Trypanosoma brucei enolase: visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition. J Mol Biol, 331, 653-665. PubMed id: 12899835 DOI: 10.1016/S0022-2836(03)00752-6
Date:
28-Mar-03     Release date:   02-Apr-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9NDH8  (Q9NDH8_TRYBB) -  Enolase
Seq:
Struc:
429 a.a.
422 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
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
+ 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     phosphopyruvate hydratase complex   1 term 
  Biological process     glycolysis   1 term 
  Biochemical function     lyase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0022-2836(03)00752-6 J Mol Biol 331:653-665 (2003)
PubMed id: 12899835  
 
 
The crystal structure of Trypanosoma brucei enolase: visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition.
M.T.da Silva Giotto, V.Hannaert, D.Vertommen, M.V.de A S Navarro, M.H.Rider, P.A.Michels, R.C.Garratt, D.J.Rigden.
 
  ABSTRACT  
 
The glycolytic enzymes of the trypanosomatids, that cause a variety of medically and agriculturally important diseases, are validated targets for drug design. Design of species-specific inhibitors is facilitated by the availability of structural data. Irreversible inhibitors, that bound covalently to the parasite enzyme alone, would be potentially particularly effective. Here we determine the crystal structure of enolase from Trypanosoma brucei and show that two cysteine residues, located in a water-filled cavity near the active-site, are modified by iodoacetamide leading to loss of catalytic activity. Since these residues are specific to the Trypanosomatidae lineage, this finding opens the way for the development of parasite-specific, irreversibly binding enolase inhibitors. In the present structure, the catalytic site is partially occupied by sulphate and two zinc ions. Surprisingly, one of these zinc ions illustrates the existence of a novel enolase-binding site for divalent metals. Evidence suggests that this is the first direct visualization of the elusive inhibitory metal site, whose existence has hitherto only been inferred from kinetic data.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Overall structural representation of a T. brucei enolase monomer. Helices and strands are coloured red and yellow, respectively. Coil regions are shown in green in the N-terminal domain and cyan in the barrel domain. The loop regions whose conformations depend on binding to the catalytic site, are shown in magenta and labelled 1-3. Residues bordering the two stretches for which electron density did not permit modelling are labelled. The bound sulphate is shown as ball and stick and the two bound Zn2+ ions, in the labelled sites I and III, as isolated white spheres. The figure was made with PYMOL/-, as were Figure 3, Figure 4 and Figure 5.
Figure 5.
Figure 5. (a) Coordination of the Zn2+ ions (isolated white spheres) in sites I and III. Hydrogen bonds are shown as dotted lines. Also shown are the relative positions of Cys147 and Cys241, the pair of buried water molecules (isolated blue spheres; see the text), and the bound sulphate. For comparison, the locations of bound PGA (pink) and Mg2+ in site II (magenta) are shown from the superposed complex of yeast enolase, two Mg2+ and substrate (PDB code 1one[14]). Electron density is shown for T. brucei enolase ligands in a simulated annealing omit |F[o] -F[c]| map obtained after their exclusion. Density is contoured at levels of 5s (blue) and 7s (purple) for the sulphate and Zn2+ ions, respectively. (b) Positioning of the metal sites and selected residues, including Cys147 and Cys241, relative to the overall structure of the large domain. For clarity neither the small domain, nor the helices that, in this orientation, lie in front of the barrel are shown. The orientation is the same as in Figure 5(a). The colours of ligands and residues are the same as in Figure 5(a) while secondary structure is coloured as in Figure 3.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 653-665) copyright 2003.  
  Figures were selected by an automated process.  

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.  
20127115 W.Gan, G.Zhao, H.Xu, W.Wu, W.Du, J.Huang, X.Yu, and X.Hu (2010).
Reverse vaccinology approach identify an Echinococcus granulosus tegumental membrane protein enolase as vaccine candidate.
  Parasitol Res, 106, 873-882.  
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
  18997349 H.Yamamoto, and N.Kunishima (2008).
Purification, crystallization and preliminary crystallographic study of the putative enolase MJ0232 from the hyperthermophilic archaeon Methanococcus jannaschii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1087-1090.  
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
15096219 D.G.Guerra, D.Vertommen, L.A.Fothergill-Gilmore, F.R.Opperdoes, and P.A.Michels (2004).
Characterization of the cofactor-independent phosphoglycerate mutase from Leishmania mexicana mexicana. Histidines that coordinate the two metal ions in the active site show different susceptibilities to irreversible chemical modification.
  Eur J Biochem, 271, 1798-1810.  
15606772 I.Pal-Bhowmick, K.Sadagopan, H.K.Vora, A.Sehgal, S.Sharma, and G.K.Jarori (2004).
Cloning, over-expression, purification and characterization of Plasmodium falciparum enolase.
  Eur J Biochem, 271, 4845-4854.  
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.  
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.