1NI4

HUMAN PYRUVATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase

Ciszak, E.M.Korotchkina, L.G.Dominiak, P.M.Sidhu, S.Patel, M.S.

(2003) J.Biol.Chem. 278: 21240-21246

  • DOI: 10.1074/jbc.M300339200

  • PubMed Abstract: 
  • The derivative of vitamin B1, thiamin pyrophosphate, is a cofactor of enzymes performing catalysis in pathways of energy production. In alpha2beta2-heterotetrameric human pyruvate dehydrogenase, this cofactor is used to cleave the Calpha-C(=O) bond o ...

    The derivative of vitamin B1, thiamin pyrophosphate, is a cofactor of enzymes performing catalysis in pathways of energy production. In alpha2beta2-heterotetrameric human pyruvate dehydrogenase, this cofactor is used to cleave the Calpha-C(=O) bond of pyruvate followed by reductive acetyl transfer to lipoyl-dihydrolipoamide acetyltransferase. The dynamic nonequivalence of two, otherwise chemically equivalent, catalytic sites has not yet been understood. To understand the mechanism of action of this enzyme, we determined the crystal structure of the holo-form of human pyruvate dehydrogenase at 1.95-A resolution. We propose a model for the flip-flop action of this enzyme through a concerted approximately 2-A shuttle-like motion of its heterodimers. Similarity of thiamin pyrophosphate binding in human pyruvate dehydrogenase with functionally related enzymes suggests that this newly defined shuttle-like motion of domains is common to the family of thiamin pyrophosphate-dependent enzymes.


    Related Citations: 
    • Molecular cloning and characterization of human pyruvate dehydrogenase beta subunit gene.
      Koike, K.,Urata, Y.,Koike, M.
      (1990) Proc.Natl.Acad.Sci.USA 87: 5594


    Organizational Affiliation

    Biological and Physical Space Research Laboratory, National Aeronautics and Space Administration/Marshall Space Flight Center and Universities Space Research Association, Huntsville, Alabama 35812, USA. Ewa.M.Ciszak@nasa.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate dehydrogenase E1 component: Alpha subunit
A, C
365Homo sapiensGene Names: PDHA1 (PHE1A)
EC: 1.2.4.1
Find proteins for P08559 (Homo sapiens)
Go to Gene View: PDHA1
Go to UniProtKB:  P08559
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pyruvate dehydrogenase E1 component: Beta subunit
B, D
341Homo sapiensGene Names: PDHB (PHE1B)
EC: 1.2.4.1
Find proteins for P11177 (Homo sapiens)
Go to Gene View: PDHB
Go to UniProtKB:  P11177
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, C
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.337α = 90.00
b = 126.889β = 90.00
c = 190.638γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing
MOLREPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance