3DV0

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex

Pei, X.Y.Titman, C.M.Frank, R.A.Leeper, F.J.Luisi, B.F.

(2008) Structure 16: 1860-1872

  • DOI: https://doi.org/10.1016/j.str.2008.10.009
  • Primary Citation of Related Structures:  
    3DUF, 3DV0, 3DVA

  • PubMed Abstract: 

    The pyruvate dehydrogenase multienzyme assembly (PDH) generates acetyl coenzyme A and reducing equivalents from pyruvate in a multiple-step process that is a nexus of central metabolism. We report crystal structures of the Geobacillus stearothermophilus PDH E1p subunit with ligands that mimic the prereaction complex and the postdecarboxylation product. The structures implicate residues that help to orient substrates, nurture intermediates, and organize surface loops so that they can engage a mobile lipoyl domain that receives the acetyl group and shuttles it to the next active site. The structural and enzymatic data suggest that H128beta performs a dual role: first, as electrostatic catalyst of the reaction of pyruvate with the thiamine cofactor; and second, as a proton donor in the second reaction of acetyl group with the lipoate. We also identify I206alpha as a key residue in mediating the conformation of active-site loops. We propose that a simple conformational flip of the H271alpha side chain assists transfer of the acetyl group from thiamine cofactor to lipoyl domain in synchrony with reduction of the dithiolane ring.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate dehydrogenase E1 component subunit alpha
A, C, E, G
369N/AMutation(s): 0 
Gene Names: pdhA
EC: 1.2.4.1
UniProt
Find proteins for P21873 (Geobacillus stearothermophilus)
Explore P21873 
Go to UniProtKB:  P21873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21873
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate dehydrogenase E1 component subunit beta
B, D, F, H
325N/AMutation(s): 0 
Gene Names: pdhB
EC: 1.2.4.1
UniProt
Find proteins for P21874 (Geobacillus stearothermophilus)
Explore P21874 
Go to UniProtKB:  P21874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21874
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
I, J
428N/AMutation(s): 0 
Gene Names: pdhC
EC: 2.3.1.12
UniProt
Find proteins for P11961 (Geobacillus stearothermophilus)
Explore P11961 
Go to UniProtKB:  P11961
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11961
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPW
Query on TPW

Download Ideal Coordinates CCD File 
L [auth A],
Q [auth C],
T [auth E],
X [auth G]
2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
C13 H19 N3 O7 P2 S
IOGGWTLVIZLGGZ-UHFFFAOYSA-N
PYR
Query on PYR

Download Ideal Coordinates CCD File 
O [auth B],
S [auth D]
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
M [auth B],
R [auth D],
V [auth F],
Z [auth H]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth A]
N [auth B]
P [auth C]
U [auth E]
W [auth G]
K [auth A],
N [auth B],
P [auth C],
U [auth E],
W [auth G],
Y [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.312α = 90
b = 232.82β = 91.83
c = 92.004γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection