2J9F

Human branched-chain alpha-ketoacid dehydrogenase-decarboxylase E1b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Two Active Sites in Human Branched-Chain Alpha- Keto Acid Dehydrogenase Operate Independently without an Obligatory Alternating-Site Mechanism.

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

(2007) J.Biol.Chem. 282: 11904

  • DOI: 10.1074/jbc.M610843200

  • PubMed Abstract: 
  • A long standing controversy is whether an alternating activesite mechanism occurs during catalysis in thiamine diphosphate (ThDP)-dependent enzymes. We address this question by investigating the ThDP-dependent decarboxylase/dehydrogenase (E1b) compon ...

    A long standing controversy is whether an alternating activesite mechanism occurs during catalysis in thiamine diphosphate (ThDP)-dependent enzymes. We address this question by investigating the ThDP-dependent decarboxylase/dehydrogenase (E1b) component of the mitochondrial branched-chain alpha-keto acid dehydrogenase complex (BCKDC). Our crystal structure reveals that conformations of the two active sites in the human E1b heterotetramer harboring the reaction intermediate are identical. Acidic residues in the core of the E1b heterotetramer, which align with the proton-wire residues proposed to participate in active-site communication in the related pyruvate dehydrogenase from Bacillus stearothermophilus, are mutated. Enzyme kinetic data show that, except in a few cases because of protein misfolding, these alterations are largely without effect on overall activity of BCKDC, ruling out the requirement of a proton-relay mechanism in E1b. BCKDC overall activity is nullified at 50% phosphorylation of E1b, but it is restored to nearly half of the pre-phosphorylation level after dissociation and reconstitution of BCKDC with the same phosphorylated E1b. The results suggest that the abolition of overall activity likely results from the specific geometry of the half-phosphorylated E1b in the BCKDC assembly and not due to a disruption of the alternating active-site mechanism. Finally, we show that a mutant E1b containing only one functional active site exhibits half of the wild-type BCKDC activity, which directly argues against the obligatory communication between active sites. The above results provide evidence that the two active sites in the E1b heterotetramer operate independently during the ThDP-dependent decarboxylation reaction.


    Related Citations: 
    • A Versatile Conformational Switch Regulates Reactivity in Human Branched-Chain Alpha-Ketoacid Dehydrogenase
      Machius, M.,Wynn, R.M.,Chuang, J.L.,Li, J.,Kluger, R.,Yu, D.,Tomchick, D.R.,Brautigam, C.A.,Chuang, D.T.
      (2006) Structure 14: 287
    • Cross-Talk between Thiamin Diphosphate Binding and Phosphorylation Loop Conformation in Human Branched-Chain Alpha-Keto Acid 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 Active Site and Novel K+ Ion-Binding Site Residues in Human Mitochondrial Branched-Chain Alpha-Ketoacid Decarboxylase/Dehydrogenase.
      Wynn, R.M.,Ho, R.,Chuang, J.L.,Chuang, D.T.
      (2001) J.Biol.Chem. 276: 4168


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
A, C
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, D
350Homo 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, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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

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Download CCD File 
A, C
C2-1-HYDROXY-3-METHYL-PROPYL-THIAMIN DIPHOSPHATE
C16 H26 N4 O8 P2 S
VBABUKBBNKNHAI-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.342α = 90.00
b = 145.342β = 90.00
c = 138.050γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2011-06-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance