2XTA | pdb_00002xta

Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase in complex with acetyl-CoA (triclinic form)

• PDB DOI: https://doi.org/10.2210/pdb2XTA/pdb

• Classification: LYASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-10-05 Released: 2011-06-15 
• Deposition Author(s): Wagner, T., Bellinzoni, M., Wehenkel, A.M., O'Hare, H.M., Alzari, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.214 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism.

Wagner, T., Bellinzoni, M., Wehenkel, A.M., O'Hare, H.M., Alzari, P.M.

(2011) Chem Biol 18: 1011

• PubMed: 21867916 
• DOI: https://doi.org/10.1016/j.chembiol.2011.06.004
• Primary Citation Related Structures: 
  2XT6, 2XTA, 2Y0P, 2YIC, 2YID


• PubMed Abstract: 
  

  The α-ketoglutarate dehydrogenase (KDH) complex is a major regulatory point of aerobic energy metabolism. Mycobacterium tuberculosis was reported to lack KDH activity, and the putative KDH E1o component, α-ketoglutarate decarboxylase (KGD), was instead assigned as a decarboxylase or carboligase. Here, we show that this protein does in fact sustain KDH activity, as well as the additional two reactions, and these multifunctional properties are shared by the Escherichia coli homolog, SucA. We also show that the mycobacterial enzyme is finely regulated by an additional acyltransferase-like domain and by the action of acetyl-CoA, a powerful allosteric activator able to enhance the concerted protein motions observed during catalysis. Our results uncover the functional plasticity of a crucial node in bacterial metabolism, which may be important for M. tuberculosis during host infection.

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Organizational Affiliation: 
• Institut Pasteur, Unité de Biochimie Structurale (CNRS URA 2185), 25 rue du Dr. Roux, 75724 Paris, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 393.05 kDa 
• Atom Count: 26,097 
• Modeled Residue Count: 3,275 
• Deposited Residue Count: 3,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-OXOGLUTARATE DECARBOXYLASE	A, B, C, D	868	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  EC: 4.1.1.71 (PDB Primary Data), 2.3.1.61 (UniProt), 2.2.1.5 (UniProt), 1.2.4.2 (UniProt)
UniProt
Find proteins for A0R2B1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R2B1  Go to UniProtKB:  A0R2B1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	H [auth A], O [auth C], S [auth D]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
TPP	E [auth A], I [auth B], L [auth C], P [auth D]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
CA	G [auth A], K [auth B], N [auth C], R [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	F [auth A], J [auth B], M [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.214 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.55	α = 99.59
b = 83.58	β = 98.94
c = 160.07	γ = 100.68

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Wagner, T., Bellinzoni, M., Wehenkel, A.M., O'Hare, H.M., Alzari, P.M.

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-10-12
  Changes: Database references, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description