1EBG

CHELATION OF SER 39 TO MG2+ LATCHES A GATE AT THE ACTIVE SITE OF ENOLASE: STRUCTURE OF THE BIS(MG2+) COMPLEX OF YEAST ENOLASE AND THE INTERMEDIATE ANALOG PHOSPHONOACETOHYDROXAMATE AT 2.1 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.186 

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This is version 1.2 of the entry. See complete history


Literature

Chelation of serine 39 to Mg2+ latches a gate at the active site of enolase: structure of the bis(Mg2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-A resolution.

Wedekind, J.E.Poyner, R.R.Reed, G.H.Rayment, I.

(1994) Biochemistry 33: 9333-9342

  • DOI: 10.1021/bi00197a038
  • Primary Citation of Related Structures:  
    1EBG

  • PubMed Abstract: 
  • The structure of a new crystal form of enolase from bakers' yeast has been solved to 2.1-A resolution. Crystals were grown from poly(ethylene glycol) and KCl at pH 8.2 in the presence of Mg2+ and a reaction intermediate analog, phosphonoacetohydroxamate (PhAH) ...

    The structure of a new crystal form of enolase from bakers' yeast has been solved to 2.1-A resolution. Crystals were grown from poly(ethylene glycol) and KCl at pH 8.2 in the presence of Mg2+ and a reaction intermediate analog, phosphonoacetohydroxamate (PhAH). Crystals belong to space group C2; have unit cell dimensions a = 123.5 A, b = 73.9 A, and c = 94.8 A with beta = 93.3 degrees; and contain one dimer per asymmetric unit. The structure was solved by molecular replacement from the X-ray coordinates of apoenolase [Stec, B., & Lebioda, L. (1990) J. Mol. Biol. 211, 235-248]. Both essential divalent metal ions are observed to be complexed with the inhibitor. The two Mg2+ ions are 4.05 A apart and are bridged by a mu-oxyl ligand from the carbonyl moiety of PhAH. The "high-affinity" Mg2+ coordinates to the carboxylate side chains of Asp 246, Glu 295, and Asp 320, one water molecule, and the hydroxamate and carbonyl oxygens of PhAH. The second Mg2+ coordinates to a phosphonyl oxygen, two water molecules, and the mu-bridge carbonyl oxygen of PhAH. Coordination schemes with respect to PhAH and water ligands are fully consistent with those of the Mn2+ complexes determined spectroscopically [Poyner, R.R., & Reed, G. H. (1992) Biochemistry 31, 7166-7173]. Remaining ligands for the second Mg2+ are the carbonyl oxygen and gamma-oxygen of Ser 39. Chelation of this Ser residue to Mg2+ effectively "latches" a flexible loop extending from Gly 37 through His 43 and closes off the entrance to the active site. The position of the second Mg2+ in the active site provides new insight into the stereochemistry of substrate binding.


    Organizational Affiliation

    Institute for Enzyme Research, Graduate School, University of Wisconsin, Madison 53705.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENOLASEA, B436Saccharomyces cerevisiaeMutation(s): 0 
EC: 4.2.1.11
UniProt
Find proteins for P00924 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00924 
Go to UniProtKB:  P00924
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00924
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PAH Binding MOAD:  1EBG Ki: 0.02 (nM) from 1 assay(s)
PDBBind:  1EBG Ki: 0.02 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.5α = 90
b = 73.9β = 93.3
c = 94.8γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-04-27
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance