3EXH

Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.444 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.

Kato, M.Wynn, R.M.Chuang, J.L.Tso, S.C.Machius, M.Li, J.Chuang, D.T.

(2008) Structure 16: 1849-1859

  • DOI: 10.1016/j.str.2008.10.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the crystal structures of the phosporylated pyruvate dehydrogenase (E1p) component of the human pyruvate dehydrogenase complex (PDC). The complete phosphorylation at Ser264-alpha (site 1) of a variant E1p protein was achieved using robust p ...

    We report the crystal structures of the phosporylated pyruvate dehydrogenase (E1p) component of the human pyruvate dehydrogenase complex (PDC). The complete phosphorylation at Ser264-alpha (site 1) of a variant E1p protein was achieved using robust pyruvate dehydrogenase kinase 4 free of the PDC core. We show that unlike its unmodified counterpart, the presence of a phosphoryl group at Ser264-alpha prevents the cofactor thiamine diphosphate-induced ordering of the two loops carrying the three phosphorylation sites. The disordering of these phosphorylation loops is caused by a previously unrecognized steric clash between the phosphoryl group at site 1 and a nearby Ser266-alpha, which nullifies a hydrogen-bonding network essential for maintaining the loop conformations. The disordered phosphorylation loops impede the binding of lipoyl domains of the PDC core to E1p, negating the reductive acetylation step. This results in the disruption of the substrate channeling in the PDC, leading to the inactivation of this catalytic machine.


    Organizational Affiliation

    Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9038, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
A, E
382Homo sapiensMutation(s): 2 
Gene 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 subunit beta, mitochondrial
B, D, F, H
329Homo sapiensMutation(s): 0 
Gene Names: PDHB (PHE1B)
EC: 1.2.4.1
Find proteins for P11177 (Homo sapiens)
Go to Gene View: PDHB
Go to UniProtKB:  P11177
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
C, G
382Homo sapiensMutation(s): 2 
Gene Names: PDHA1 (PHE1A)
EC: 1.2.4.1
Find proteins for P08559 (Homo sapiens)
Go to Gene View: PDHA1
Go to UniProtKB:  P08559
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C, E, G
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
TPP
Query on TPP

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

Download SDF File 
Download CCD File 
A, C, E, G
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C, E, G
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
C, G
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TPPKd: 13100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.444 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 257.064α = 90.00
b = 115.612β = 113.64
c = 127.592γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description