1W88

The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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Literature

A Molecular Switch and Proton-Wire Synchronize the Active Sites in Thiamine-Dependent Enzymes

Frank, R.A.W.Titman, C.M.Pratap, J.V.Luisi, B.F.Perham, R.N.

(2004) Science 306: 872

  • DOI: 10.1126/science.1101030
  • Primary Citation of Related Structures:  
    1W85, 1W88

  • PubMed Abstract: 
  • Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein ...

    Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein. This "proton wire" permits the co-factors to serve reciprocally as general acid/base in catalysis and to switch the conformation of crucial active-site peptide loops. This synchronizes the progression of chemical events and can account for the oligomeric organization, conformational asymmetry, and "ping-pong" kinetic properties of E1 and other thiamine-dependent enzymes.


    Related Citations: 
    • Molecular Assembly of a Multi-Enzymes Complex: The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2
      Frank, R.A.W., Pratap, J.V., Pei, X.Y., Perham, R.N., Luisi, B.F.
      () To be published --: --

    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNITA, C, E, G368Geobacillus stearothermophilusMutation(s): 2 
Gene Names: pdhA
EC: 1.2.4.1
UniProt
Find proteins for P21873 (Geobacillus stearothermophilus)
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Go to UniProtKB:  P21873
Entity Groups  
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UniProt GroupP21873
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNITB, D, F, H324Geobacillus stearothermophilusMutation(s): 0 
Gene Names: pdhB
EC: 1.2.4.1
UniProt
Find proteins for P21874 (Geobacillus stearothermophilus)
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UniProt GroupP21874
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATEI, J49Geobacillus stearothermophilusMutation(s): 0 
Gene Names: pdhC
EC: 2.3.1.12
UniProt
Find proteins for P11961 (Geobacillus stearothermophilus)
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Go to UniProtKB:  P11961
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UniProt GroupP11961
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.18α = 90
b = 133.69β = 90
c = 245.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary