PDBsum entry 1p48

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
Protein chains
436 a.a. *
PEP ×2
_MG ×4
Waters ×743
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Reverse protonation is the key to general acid-base catalysis in enolase
Structure: Enolase 1. Chain: a, b. Synonym: 2-phosphoglycerate dehydratase, 2-phospho-d- glycerate hydro-lyase. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: eno1 or enoa or hsp48 or ygr254w or g9160. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.185     R-free:   0.213
Authors: P.A.Sims,T.M.Larsen,R.R.Poyner,W.W.Cleland,G.H.Reed
Key ref:
P.A.Sims et al. (2003). Reverse protonation is the key to general acid-base catalysis in enolase. Biochemistry, 42, 8298-8306. PubMed id: 12846578 DOI: 10.1021/bi0346345
21-Apr-03     Release date:   18-Nov-03    
Go to PROCHECK summary

Protein chains
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 = PEP)
corresponds exactly
+ 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/bi0346345 Biochemistry 42:8298-8306 (2003)
PubMed id: 12846578  
Reverse protonation is the key to general acid-base catalysis in enolase.
P.A.Sims, T.M.Larsen, R.R.Poyner, W.W.Cleland, G.H.Reed.
The pH dependence of enolase catalysis was studied to understand how enolase is able to utilize both general acid and general base catalysis in each direction of the reaction at near-neutral pHs. Wild-type enolase from yeast was assayed in the dehydration reaction (2-phospho-D-glycerate --> phosphoenolpyruvate + H(2)O) at different pHs. E211Q, a site-specific variant of enolase that catalyzes the exchange of the alpha-proton of 2-phospho-D-glycerate but not the complete dehydration, was assayed in a (1)H/(2)H exchange reaction at different pDs. Additionally, crystal structures of E211Q and E168Q were obtained at 2.0 and 1.8 A resolution, respectively. Analysis of the pH profile of k(cat)/K(Mg) for wild-type enolase yielded macroscopic pK(a) estimates of 7.4 +/- 0.3 and 9.0 +/- 0.3, while the results of the pD profile of the exchange reaction of E211Q led to a pK(a) estimate of 9.5 +/- 0.1. These values permit estimates of the four microscopic pK(a)s that describe the four relevant protonation states of the acid/base catalytic groups in the active site. The analysis indicates that the dehydration reaction is catalyzed by a small fraction of enzyme that is reverse-protonated (i.e., Lys345-NH(2), Glu211-COOH), whereas the hydration reaction is catalyzed by a larger fraction of the enzyme that is typically protonated (i.e., Lys345-NH(3)(+), Glu211-COO(-)). These two forms of the enzyme coexist in a constant, pH-independent ratio. The structures of E211Q and E168Q both show virtually identical folds and active-site architectures (as compared to wild-type enolase) and thus provide additional support to the conclusions reported herein. Other enzymes that require both general acid and general base catalysis likely require reverse protonation of catalytic groups in one direction of the reaction.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20593474 K.W.Clancy, J.A.Melvin, and D.G.McCafferty (2010).
Sortase transpeptidases: insights into mechanism, substrate specificity, and inhibition.
  Biopolymers, 94, 385-396.  
19309142 M.A.Spies, J.G.Reese, D.Dodd, K.L.Pankow, S.R.Blanke, and J.Baudry (2009).
Determinants of catalytic power and ligand binding in glutamate racemase.
  J Am Chem Soc, 131, 5274-5284.  
19371088 M.L.Raber, S.O.Arnett, and C.A.Townsend (2009).
A conserved tyrosyl-glutamyl catalytic dyad in evolutionarily linked enzymes: carbapenam synthetase and beta-lactam synthetase.
  Biochemistry, 48, 4959-4971.  
17822439 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
16301798 Z.Q.Fu (2005).
Three-dimensional model-free experimental error correction of protein crystal diffraction data with free-R test.
  Acta Crystallogr D Biol Crystallogr, 61, 1643-1648.  
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