1W88

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

• PDB DOI: https://doi.org/10.2210/pdb1W88/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-09-16 Released: 2004-11-02 
• Deposition Author(s): Frank, R.A.W., Pratap, J.V., Pei, X.Y., Perham, R.N., Luisi, B.F.

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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 

Starting Model: experimental

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

• PubMed: 15514159 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 319.32 kDa 
• Atom Count: 21,934 
• Modelled Residue Count: 2,701 
• Deposited Residue Count: 2,866 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT	A, C, E, G	368	Geobacillus stearothermophilus	Mutation(s): 2  EC: 1.2.4.1
UniProt
Find proteins for P21873 (Geobacillus stearothermophilus) Explore P21873  Go to UniProtKB:  P21873

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT	B, D, F, H	324	Geobacillus stearothermophilus	Mutation(s): 0  EC: 1.2.4.1
UniProt
Find proteins for P21874 (Geobacillus stearothermophilus) Explore P21874  Go to UniProtKB:  P21874

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE	I, J	49	Geobacillus stearothermophilus	Mutation(s): 0  EC: 2.3.1.12
UniProt
Find proteins for P11961 (Geobacillus stearothermophilus) Explore P11961  Go to UniProtKB:  P11961

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	L [auth A], N [auth C], P [auth E], R [auth G]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
MG	K [auth A], M [auth C], O [auth E], Q [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 92.18	α = 90
b = 133.69	β = 90
c = 245.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-02 
Deposition Author(s): Frank, R.A.W., Pratap, J.V., Pei, X.Y., Perham, R.N., Luisi, B.F.

Revision History  

• 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
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description