PDBsum entry 2al1

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
Protein chains
436 a.a. *
PEP ×2
_MG ×4
__K ×2
Waters ×705
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure analysis of enolase mg subunit complex at ph 8.0
Structure: Enolase 1. Chain: a, b. Synonym: 2-phosphoglycerate dehydratase. 2-phospho-d- glycerate hydro-lyase. Ec:
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Other_details: genes eno1, enoa, hsp48
Biol. unit: Dimer (from PQS)
1.50Å     R-factor:   0.153     R-free:   0.217
Authors: P.A.Sims,A.L.Menefee,T.M.Larsen,S.O.Mansoorabadi,G.H.Reed
Key ref:
P.A.Sims et al. (2006). Structure and catalytic properties of an engineered heterodimer of enolase composed of one active and one inactive subunit. J Mol Biol, 355, 422-431. PubMed id: 16309698 DOI: 10.1016/j.jmb.2005.10.050
04-Aug-05     Release date:   24-Jan-06    
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 1 residue position (black cross)

 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
Bound ligand (Het Group name = PEP)
corresponds exactly
+ H(2)O
      Cofactor: Magnesium
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: 10.1016/j.jmb.2005.10.050 J Mol Biol 355:422-431 (2006)
PubMed id: 16309698  
Structure and catalytic properties of an engineered heterodimer of enolase composed of one active and one inactive subunit.
P.A.Sims, A.L.Menefee, T.M.Larsen, S.O.Mansoorabadi, G.H.Reed.
Enolase is a dimeric enzyme that catalyzes the interconversion of 2-phospho-D-glycerate and phosphoenolpyruvate. This reversible dehydration is effected by general acid-base catalysis that involves, principally, Lys345 and Glu211 (numbering system of enolase 1 from yeast). The crystal structure of the inactive E211Q enolase shows that the protein is properly folded. However, K345 variants have, thus far, failed to crystallize. This problem was solved by crystallization of an engineered heterodimer of enolase. The heterodimer was composed of an inactive subunit that has a K345A mutation and an active subunit that has N80D and N126D surface mutations to facilitate ion-exchange chromatographic separation of the three dimeric species. The structure of this heterodimeric variant, in complex with substrate/product, was obtained at 1.85 A resolution. The structure was compared to a new structure of wild-type enolase obtained from crystals belonging to the same space group. Asymmetric dimers having one subunit exhibiting two of the three active site loops in an open conformation and the other in a conformation having all three loops closed appear in both structures. The K345A subunit of the heterodimer is in the loop-closed conformation; its Calpha carbon atoms closely match those of the corresponding subunit of wild-type enolase (root-mean-squared deviation of 0.23 A). The kcat and kcat/Km values of the heterodimer are approximately half those of the N80D/N126D homodimer, which suggests that the subunits in solution are kinetically independent. A comparison of enolase structures obtained from crystals belonging to different space groups suggests that asymmetric dimers can be a consequence of the asymmetric positioning of the subunits within the crystal lattice.
  Selected figure(s)  
Figure 3.
Figure 3. Stereoview of a ribbon representation of the K345A subunit (teal). An overlay of the K345A subunit and the wt* subunit shows that the loop regions are the only regions of significant difference. Loop 1 (residues 37-43) is labeled L1. Loop 2 (residues 153-166) is labeled L2. Loop 3 (residues 251-275) is labeled L3. The violet loops represent the K345A subunit and the red loops (parts of which are disordered) represent the wt* subunit. The 2-PGA, shown in ball and stick representation, and the magnesium ions, shown as green spheres, are from the K345A subunit. The C terminus is labeled C and the N terminus is labeled N.
Figure 5.
Figure 5. Stereoview of key active-site residues for the K345A subunit. The F[o]-F[c] electron density map, contoured at 3.7s, is shown for 2-PGA.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 355, 422-431) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19655245 S.H.Tu, C.C.Chang, C.S.Chen, K.W.Tam, Y.J.Wang, C.H.Lee, H.W.Lin, T.C.Cheng, C.S.Huang, J.S.Chu, N.Y.Shih, L.C.Chen, S.J.Leu, Y.S.Ho, and C.H.Wu (2010).
Increased expression of enolase alpha in human breast cancer confers tamoxifen resistance in human breast cancer cells.
  Breast Cancer Res Treat, 121, 539-553.  
17603476 M.Szczepek, V.Brondani, J.Büchel, L.Serrano, D.J.Segal, and T.Cathomen (2007).
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases.
  Nat Biotechnol, 25, 786-793.  
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
17367133 R.Carmieli, T.M.Larsen, G.H.Reed, S.Zein, F.Neese, and D.Goldfarb (2007).
The catalytic Mn2+ sites in the enolase-inhibitor complex: crystallography, single-crystal EPR, and DFT calculations.
  J Am Chem Soc, 129, 4240-4252.  
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 codes are shown on the right.