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 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1NI4

  • 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 of py ...

    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 U S A 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate dehydrogenase E1 component: Alpha subunit A, C365Homo sapiensMutation(s): 12 
Gene Names: PDHA1, PHE1A
EC: 1.2.4.1
Find proteins for P08559 (Homo sapiens)
Explore P08559 
Go to UniProtKB:  P08559
NIH Common Fund Data Resources
PHAROS:  P08559
GTEx:  ENSG00000131828
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate dehydrogenase E1 component: Beta subunit B, D341Homo sapiensMutation(s): 13 
Gene Names: PDHB, PHE1B
EC: 1.2.4.1
Find proteins for P11177 (Homo sapiens)
Explore P11177 
Go to UniProtKB:  P11177
NIH Common Fund Data Resources
PHAROS:  P11177
GTEx:  ENSG00000168291
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP
Download Ideal Coordinates CCD File 
A, C
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
B, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,CL-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 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.337α = 90
b = 126.889β = 90
c = 190.638γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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