PDBsum entry 5enl

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Carbon-oxygen lyase PDB id
Protein chain
436 a.a. *
Waters ×355
* Residue conservation analysis
PDB id:
Name: Carbon-oxygen lyase
Title: Inhibition of enolase: the crystal structures of enolase- ca2+-phosphoglycerate and enolase-zn2+-phosphoglycolate complexes at 2.2-angstroms resolution
Structure: Enolase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
2.20Å     R-factor:   0.148    
Authors: L.Lebioda,B.Stec
Key ref:
L.Lebioda et al. (1991). Inhibition of enolase: the crystal structures of enolase-Ca2(+)- 2-phosphoglycerate and enolase-Zn2(+)-phosphoglycolate complexes at 2.2-A resolution. Biochemistry, 30, 2823-2827. PubMed id: 2007121 DOI: 10.1021/bi00225a013
13-Nov-90     Release date:   15-Apr-92    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00924  (ENO1_YEAST) -  Enolase 1
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.  - Phosphopyruvate hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O
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/bi00225a013 Biochemistry 30:2823-2827 (1991)
PubMed id: 2007121  
Inhibition of enolase: the crystal structures of enolase-Ca2(+)- 2-phosphoglycerate and enolase-Zn2(+)-phosphoglycolate complexes at 2.2-A resolution.
L.Lebioda, B.Stec, J.M.Brewer, E.Tykarska.
Enolase is a metalloenzyme which catalyzes the elimination of H2O from 2-phosphoglyceric acid (PGA) to form phosphoenolpyruvate (PEP). Mg2+ and Zn2+ are cofactors which strongly bind and activate the enzyme. Ca2+ also binds strongly but does not produce activity. Phosphoglycolate (PG) is a competitive inhibitor of enolase. The structures of two inhibitory ternary complexes: yeast enolase-Ca2(+)-PGA and yeast enolase-Zn2(+)-PG, were determined by X-ray diffraction to 2.2-A resolution and were refined by crystallographic least-squares to R = 14.8% and 15.7%, respectively, with good geometries of the models. These structures are compared with the structure of the precatalytic ternary complex enolase-Mg2(+)-PGA/PEP (Lebioda & Stec, 1991). In the complex enolase-Ca2(+)-PGA, the PGA molecule coordinates to the Ca2+ ion with the hydroxyl group, as in the precatalytic complex. The conformation of the PGA molecule is however different. In the active complex, the organic part of the PGA molecule is planar, similar to the product. In the inhibitory complex, the carboxylic group is in an orthonormal conformation. In the inhibitory complex enolase-Zn2(+)-PG, the PG molecule coordinates with the carboxylic group in a monodentate mode. In both inhibitory complexes, the conformational changes in flexible loops, which were observed in the precatalytic complex, do not take place. The lack of catalytic metal ion binding suggests that these conformational changes are necessary for the formation of the catalytic metal ion binding site.

Literature references that cite this PDB file's key reference

  PubMed id Reference
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
11987159 A.Bergner, J.Günther, M.Hendlich, G.Klebe, and M.Verdonk (2001).
Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects.
  Biopolymers, 61, 99.  
11114510 H.Erlandsen, E.E.Abola, and R.C.Stevens (2000).
Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites.
  Curr Opin Struct Biol, 10, 719-730.  
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
7615571 S.M.Callahan, N.W.Cornell, and P.V.Dunlap (1995).
Purification and properties of periplasmic 3':5'-cyclic nucleotide phosphodiesterase. A novel zinc-containing enzyme from the marine symbiotic bacterium Vibrio fischeri.
  J Biol Chem, 270, 17627-17632.  
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
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