Biological Assembly 1  

Global Symmetry: Octahedral - O  (3D View)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 237.69 kDa 
• Atom Count: 15,647 
• Modelled Residue Count: 1,872 
• Deposited Residue Count: 2,096 
• Unique protein chains: 1

 2II3

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

• PDB DOI:  https://doi.org/10.2210/pdb2II3/pdb

• Classification: TRANSFERASE
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-09-27 Released: 2006-12-26 
• Deposition Author(s): Kato, M., Wynn, R.M., Chuang, J.L., Brautigam, C.A., Custorio, M., Chuang, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.259 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

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

• PubMed: 17124494 
• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex	A, B, C, D, E, F, G, H	262	Bos taurus	Mutation(s): 0  Gene Names: DBT EC: 2.3.1.168
UniProt
Find proteins for P11181 (Bos taurus) Explore P11181  Go to UniProtKB:  P11181

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAO	BA [auth D], FA [auth E], K [auth A], LA [auth F], PA [auth G], Q [auth B], VA [auth H], W [auth C]	OXIDIZED COENZYME A C21 H36 N7 O17 P3 S HWMGJMKHOJKGLQ-IBOSZNHHSA-N
ACT	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]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
CAO	Binding MOAD:  2II3	Kd: 3000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 194.915	α = 90
b = 194.915	β = 90
c = 171.997	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Kato, M., Wynn, R.M., Chuang, J.L., Brautigam, C.A., Custorio, M., Chuang, D.T.

Revision History  

• 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