3EXG

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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:  
    3EXE, 3EXF, 3EXG, 3EXH, 3EXI

  • 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 pyruv ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1, 3, 5, A, C, E, G, I, 1,  3,  5,  A,  C,  E,  G,  I,  K,  M,  O,  Q,  S,  U,  W,  Y
382Homo sapiensMutation(s): 2 
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
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate dehydrogenase E1 component subunit beta, mitochondrial2, 4, 6, B, D, F, H, J, 2,  4,  6,  B,  D,  F,  H,  J,  L,  N,  P,  R,  T,  V,  X,  Z
329Homo sapiensMutation(s): 0 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.278α = 90.14
b = 128.29β = 90.05
c = 228.41γ = 90.02
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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