1QS0 | pdb_00001qs0

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 (Depositor) 
  • R-Value Work: 
    0.218 (Depositor) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 83.68 kDa 
  • Atom Count: 5,999 
  • Modeled Residue Count: 745 
  • Deposited Residue Count: 745 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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:|  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 (Depositor) 
  • R-Value Work:  0.218 (Depositor) 
  • R-Value Observed: 0.218 (Depositor) 
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

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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
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary