1QS0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 2.0 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 Biol 6: 785-792

  • DOI: https://doi.org/10.1038/11563
  • Primary Citation of Related Structures:  
    1QS0

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-OXOISOVALERATE DEHYDROGENASE ALPHA-SUBUNIT407Pseudomonas putidaMutation(s): 12 
EC: 1.2.4.4
UniProt
Find proteins for P09060 (Pseudomonas putida)
Explore P09060 
Go to UniProtKB:  P09060
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09060
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2-OXOISOVALERATE DEHYDROGENASE BETA-SUBUNIT338Pseudomonas putidaMutation(s): 10 
EC: 1.2.4.4
UniProt
Find proteins for P09061 (Pseudomonas putida)
Explore P09061 
Go to UniProtKB:  P09061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09061
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
D [auth A]THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
COI
Query on COI

Download Ideal Coordinates CCD File 
E [auth B]2-OXO-4-METHYLPENTANOIC ACID
C6 H10 O3
BKAJNAXTPSGJCU-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.34α = 90
b = 101.34β = 90
c = 381.23γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-18
    Type: Initial release
  • Version 1.1: 2008-01-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary