1U5B

Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation

Wynn, R.M.Kato, M.Machius, M.Chuang, J.L.Li, J.Tomchick, D.R.Chuang, D.T.

(2004) Structure 12: 2185-2196

  • DOI: 10.1016/j.str.2004.09.013
  • Primary Citation of Related Structures:  1X7W, 1X7X, 1X7Y, 1X7Z, 1X80

  • PubMed Abstract: 
  • The human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex (BCKDC) is a 4 MDa macromolecular machine comprising three catalytic components (E1b, E2b, and E3), a kinase, and a phosphatase. The BCKDC overall activity is tightly regulat ...

    The human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex (BCKDC) is a 4 MDa macromolecular machine comprising three catalytic components (E1b, E2b, and E3), a kinase, and a phosphatase. The BCKDC overall activity is tightly regulated by phosphorylation in response to hormonal and dietary stimuli. We report that phosphorylation of Ser292-alpha in the E1b active site channel results in an order-to-disorder transition of the conserved phosphorylation loop carrying the phosphoryl serine. The conformational change is triggered by steric clashes of the phosphoryl group with invariant His291-alpha that serves as an indispensable anchor for the phosphorylation loop through bound thiamin diphosphate. Phosphorylation of Ser292-alpha does not severely impede the E1b-dependent decarboxylation of alpha-ketoacids. However, the disordered loop conformation prevents phosphorylated E1b from binding the E2b lipoyl-bearing domain, which effectively shuts off the E1b-catalyzed reductive acylation reaction and therefore completely inactivates BCKDC. This mechanism provides a paradigm for regulation of mitochondrial alpha-ketoacid dehydrogenase complexes by phosphorylation.


    Related Citations: 
    • Crosstalk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain A-ketoacid decarboxylase/dehydrogenase
      Li, J.,Wynn, R.M.,Machius, M.,Chuang, J.L.,KARTHIKEYAN, S.,Tomchick, D.R.,Chuang, D.T.
      (2004) J.Biol.Chem. 279: 32968
    • Roles of His291-alpha and His146-beta in the reductive acylation reaction catalyzed by human branched-chain alpha-ketoacid dehydrogenase: refined phosphorylation loop structure in the active site
      Wynn, R.M.,Machius, M.,Chuang, J.L.,Li, J.,Tomchick, D.R.,Chuang, D.T.
      (2003) J.Biol.Chem. 278: 43402


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-oxoisovalerate dehydrogenase alpha subunit
A
400Homo sapiensGene Names: BCKDHA
EC: 1.2.4.4
Find proteins for P12694 (Homo sapiens)
Go to Gene View: BCKDHA
Go to UniProtKB:  P12694
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
2-oxoisovalerate dehydrogenase beta subunit
B
342Homo sapiensGene Names: BCKDHB
EC: 1.2.4.4
Find proteins for P21953 (Homo sapiens)
Go to Gene View: BCKDHB
Go to UniProtKB:  P21953
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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

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Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
TDP
Query on TDP

Download SDF File 
Download CCD File 
A
THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TDPKd: 1600 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.156 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.315α = 90.00
b = 143.315β = 90.00
c = 69.294γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
AMoREphasing
CNSrefinement
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance