Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: equilibrium centrifugation, SAXS

Macromolecule Content

• Total Structure Weight: 24.89 kDa 
• Atom Count: 2037 
• Modelled Residue Count: 224 
• Deposited Residue Count: 231 
• Unique protein chains: 1

6ZZN

Crystal structure of the cubic catalytic core of the Mycobacterium tuberculosis branched-chain alphaketoacid acyltransferase component (E2b).

• PDB DOI: 10.2210/pdb6ZZN/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-04 Released: 2021-08-18 
• Deposition Author(s): Vilela, P., Bellinzoni, M.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.193 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Literature

Actinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex.

Bruch, E.M., Vilela, P., Yang, L., Boyko, A., Lexa-Sapart, N., Raynal, B., Alzari, P.M., Bellinzoni, M.

(2021) Proc Natl Acad Sci U S A 118

• PubMed: 34819376 
• DOI: 10.1073/pnas.2112107118
• Primary Citation of Related Structures:  
  6ZZI, 6ZZJ, 6ZZK, 6ZZL, 6ZZM, 6ZZN


• PubMed Abstract: 
  

α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, all considered to be structured around a high-molecular weight hollow core, consisting of up to 60 subunits of the acyltransferase component. We provide here evidence that Actinobacteria break the rule by possessing an acetyltranferase component reduced to its minimally active, trimeric unit, characterized by a unique C-terminal helix bearing an actinobacterial specific insertion that precludes larger protein oligomerization. This particular feature, together with the presence of an odhA gene coding for both the decarboxylase and the acyltransferase domains on the same polypetide, is spread over Actinobacteria and reflects the association of PDH and ODH into a single physical complex. Considering the central role of the pyruvate and 2-oxoglutarate nodes in central metabolism, our findings pave the way to both therapeutic and metabolic engineering applications.

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Organizational Affiliation: 

Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, 75015 Paris, France; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex	A	231	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: bkdC, pdhC, Rv2495c EC: 2.3.1.168
UniProt
Find proteins for O06159 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O06159  Go to UniProtKB:  O06159

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ACT	B [auth A], C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.193 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 214.073	α = 90
b = 214.073	β = 90
c = 214.073	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-08-04 
• Released Date: 2021-08-18 
Deposition Author(s): Vilela, P., Bellinzoni, M.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-13-JSV8-0003

Revision History  

• Version 1.0: 2021-08-18
  Type: Initial release
  
• Version 1.1: 2021-12-08
  Changes: Database references
• Version 1.2: 2021-12-15
  Changes: Structure summary