1QS0

Crystal Structure of Pseudomonas Putida 2-oxoisovalerate Dehydrogenase (Branched-Chain Alpha-Keto Acid Dehydrogenase, E1B)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of 2-oxoisovalerate and dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes.

Aevarsson, A.Seger, K.Turley, S.Sokatch, J.R.Hol, W.G.

(1999) Nat.Struct.Mol.Biol. 6: 785-792

  • DOI: 10.1038/11563

  • PubMed Abstract: 
  • The family of giant multienzyme complexes metabolizing pyruvate, 2-oxoglutarate, branched-chain 2-oxo acids or acetoin contains several of the largest and most sophisticated protein assemblies known, with molecular masses between 4 and 10 million Da. ...

    The family of giant multienzyme complexes metabolizing pyruvate, 2-oxoglutarate, branched-chain 2-oxo acids or acetoin contains several of the largest and most sophisticated protein assemblies known, with molecular masses between 4 and 10 million Da. The principal enzyme components, E1, E2 and E3, are present in numerous copies and utilize multiple cofactors to catalyze a directed sequence of reactions via substrate channeling. The crystal structure of a heterotetrameric (alpha2beta2) E1, 2-oxoisovalerate dehydrogenase from Pseudomonas putida, reveals a tightly packed arrangement of the four subunits with the beta2-dimer held between the jaws of a 'vise' formed by the alpha2-dimer. A long hydrophobic channel, suitable to accommodate the E2 lipoyl-lysine arm, leads to the active site, which contains the cofactor thiamin diphosphate (ThDP) and an inhibitor-derived covalent modification of a histidine side chain. The E1 structure, together with previous structural information on E2 and E3, completes the picture of the shared architectural features of these enormous macromolecular assemblies.


    Organizational Affiliation

    Departments of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, P.O. Box 357742, Seattle, Washington 98195-7742, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-OXOISOVALERATE DEHYDROGENASE ALPHA-SUBUNIT
A
407Pseudomonas putidaMutation(s): 0 
Gene Names: bkdA1
EC: 1.2.4.4
Find proteins for P09060 (Pseudomonas putida)
Go to UniProtKB:  P09060
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
2-OXOISOVALERATE DEHYDROGENASE BETA-SUBUNIT
B
338Pseudomonas putidaMutation(s): 0 
Gene Names: bkdA2
EC: 1.2.4.4
Find proteins for P09061 (Pseudomonas putida)
Go to UniProtKB:  P09061
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDP
Query on TDP

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
COI
Query on COI

Download SDF File 
Download CCD File 
B
2-OXO-4-METHYLPENTANOIC ACID
alpha-ketoisocaproic acid
C6 H10 O3
BKAJNAXTPSGJCU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.340α = 90.00
b = 101.340β = 90.00
c = 381.230γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
CCP4data scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-18
    Type: Initial release
  • Version 1.1: 2008-01-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance