Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2b) component in the branched-chain alpha-ketoacid dehydrogenase complex (BCKDC), Oxidized Coenzyme A-bound form

Experimental Data Snapshot

  • Resolution: 2.17 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


A synchronized substrate-gating mechanism revealed by cubic-core structure of the bovine branched-chain alpha-ketoacid dehydrogenase complex.

Kato, M.Wynn, R.M.Chuang, J.L.Brautigam, C.A.Custorio, M.Chuang, D.T.

(2006) EMBO J 25: 5983-5994

  • DOI: https://doi.org/10.1038/sj.emboj.7601444
  • Primary Citation of Related Structures:  
    2IHW, 2II3, 2II4, 2II5

  • PubMed Abstract: 

    The dihydrolipoamide acyltransferase (E2b) component of the branched-chain alpha-ketoacid dehydrogenase complex forms a cubic scaffold that catalyzes acyltransfer from S-acyldihydrolipoamide to CoA to produce acyl-CoA. We have determined the first crystal structures of a mammalian (bovine) E2b core domain with and without a bound CoA or acyl-CoA. These structures reveal both hydrophobic and the previously unreported ionic interactions between two-fold-related trimers that build up the cubic core. The entrance of the dihydrolipoamide-binding site in a 30-A long active-site channel is closed in the apo and acyl-CoA-bound structures. CoA binding to one entrance of the channel promotes a conformational change in the channel, resulting in the opening of the opposite dihydrolipoamide gate. Binding experiments show that the affinity of the E2b core for dihydrolipoamide is markedly increased in the presence of CoA. The result buttresses the model that CoA binding is responsible for the opening of the dihydrolipoamide gate. We suggest that this gating mechanism synchronizes the binding of the two substrates to the active-site channel, which serves as a feed-forward switch to coordinate the E2b-catalyzed acyltransfer reaction.

  • Organizational Affiliation

    Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
A, B, C, D, E
A, B, C, D, E, F, G, H
262Bos taurusMutation(s): 0 
Gene Names: DBT
Find proteins for P11181 (Bos taurus)
Explore P11181 
Go to UniProtKB:  P11181
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11181
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CAO

Download Ideal Coordinates CCD File 
BA [auth D]
FA [auth E]
K [auth A]
LA [auth F]
PA [auth G]
BA [auth D],
FA [auth E],
K [auth A],
LA [auth F],
PA [auth G],
Q [auth B],
VA [auth H],
W [auth C]
C21 H36 N7 O17 P3 S
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth E]
EA [auth E]
GA [auth F]
HA [auth F]
I [auth A]
CA [auth E],
EA [auth E],
GA [auth F],
HA [auth F],
I [auth A],
KA [auth F],
L [auth B],
M [auth B],
MA [auth G],
N [auth B],
P [auth B],
QA [auth H],
R [auth C],
RA [auth H],
S [auth C],
SA [auth H],
V [auth C],
X [auth D],
Y [auth D],
Z [auth D]
C2 H3 O2
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
IA [auth F]
J [auth A]
JA [auth F]
AA [auth D],
DA [auth E],
IA [auth F],
J [auth A],
JA [auth F],
NA [auth G],
O [auth B],
OA [auth G],
T [auth C],
TA [auth H],
U [auth C],
UA [auth H]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.17 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.915α = 90
b = 194.915β = 90
c = 171.997γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description