PDBsum entry 1els

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Carbon-oxygen lyase PDB id
Protein chain
436 a.a. *
_MN ×2
Waters ×343
* Residue conservation analysis
PDB id:
Name: Carbon-oxygen lyase
Title: Catalytic metal ion binding in enolase: the crystal structur enolase-mn2+-phosphonoacetohydroxamate complex at 2.4 angst resolution
Structure: Enolase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
2.40Å     R-factor:   0.165    
Authors: E.Zhang,M.Hatada,J.M.Brewer,L.Lebioda
Key ref:
E.Zhang et al. (1994). Catalytic metal ion binding in enolase: the crystal structure of an enolase-Mn2+-phosphonoacetohydroxamate complex at 2.4-A resolution. Biochemistry, 33, 6295-6300. PubMed id: 8193144 DOI: 10.1021/bi00186a032
05-Apr-94     Release date:   31-Jul-94    
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
= 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/bi00186a032 Biochemistry 33:6295-6300 (1994)
PubMed id: 8193144  
Catalytic metal ion binding in enolase: the crystal structure of an enolase-Mn2+-phosphonoacetohydroxamate complex at 2.4-A resolution.
E.Zhang, M.Hatada, J.M.Brewer, L.Lebioda.
Enolase, a glycolytic enzyme that catalyzes the dehydration of 2-phospho-D-glycerate (PGA) to form phosphoenolpyruvate (PEP), requires two divalent metal ions per active site for activity. The first metal ion, traditionally referred to as "conformational", binds in a high-affinity site I. The second metal ion, "catalytic", binds in site II only in the presence of a substrate or substrate analogue and with much lower affinity for the physiological cofactor Mg2+. While the high-affinity site has been well characterized, the position of the lower affinity site has not been established so far. Here, we report the structure of the quaternary complex between enolase, the transition-state analogue phosphonoacetohydroxamate (PhAH), and two Mn2+ ions. The structure has been refined by using 16 561 reflections with F/sigma (F) > or = 3 to an R = 0.165 with average deviations of bond lengths and bond angles from ideal values of 0.013 A and 3.1 degrees, respectively. The "catalytic" metal ion is coordinated to two oxygen atoms of the phosphono moiety of PhAH and to the carbonyl oxygen of Gly37. Most likely, disordered water molecules complement its coordination sphere. The interaction with the site II metal ion must stabilize negative charge on the phosphate group and produce electron withdrawal from carbon 2 of the substrate, facilitating proton abstraction from carbon 2, the rate-limiting step in the catalytic process. The Gly37 residue is located in the flexible loop Ser36-His43, which assumes an "open" conformation in the absence of substrate and a "closed" conformation in the presence of a substrate.(ABSTRACT TRUNCATED AT 250 WORDS)

Literature references that cite this PDB file's key reference

  PubMed id Reference
21070651 M.Moll, D.H.Bryant, and L.E.Kavraki (2010).
The LabelHash algorithm for substructure matching.
  BMC Bioinformatics, 11, 555.  
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
15226299 J.Singh, G.A.Khan, L.Kinarsky, H.Cheng, J.Wilken, K.H.Choi, E.Bedows, S.Sherman, and P.W.Cheng (2004).
Identification of disulfide bonds among the nine core 2 N-acetylglucosaminyltransferase-M cysteines conserved in the mucin beta6-N-acetylglucosaminyltransferase family.
  J Biol Chem, 279, 38969-38977.  
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.  
10535916 S.Shan, A.Yoshida, S.Sun, J.A.Piccirilli, and D.Herschlag (1999).
Three metal ions at the active site of the Tetrahymena group I ribozyme.
  Proc Natl Acad Sci U S A, 96, 12299-12304.  
9588797 A.Hénaut, F.Lisacek, P.Nitschké, I.Moszer, and A.Danchin (1998).
Global analysis of genomic texts: the distribution of AGCT tetranucleotides in the Escherichia coli and Bacillus subtilis genomes predicts translational frameshifting and ribosomal hopping in several genes.
  Electrophoresis, 19, 515-527.  
9790688 D.A.Vinarov, and T.Nowak (1998).
pH dependence of the reaction catalyzed by yeast Mg-enolase.
  Biochemistry, 37, 15238-15246.  
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
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