6R2C

Crystal structure of the SucA domain of Mycobacterium smegmatis KGD after soaking with succinylphosphonate phosphonoethyl ester (PESP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: from a Michaelis-like complex to ThDP adducts.

Wagner, T.Boyko, A.Alzari, P.M.Bunik, V.I.Bellinzoni, M.

(2019) J.Struct.Biol. --: --

  • DOI: 10.1016/j.jsb.2019.08.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mycobacterial KGD, the thiamine diphosphate (ThDP)-dependent E1o component of the 2-oxoglutarate dehydrogenase complex (OGDHC), is known to undergo significant conformational changes during catalysis with two distinct conformational states, previousl ...

    Mycobacterial KGD, the thiamine diphosphate (ThDP)-dependent E1o component of the 2-oxoglutarate dehydrogenase complex (OGDHC), is known to undergo significant conformational changes during catalysis with two distinct conformational states, previously named as the early and late state. In this work, we employ two phosphonate analogues of 2-oxoglutarate (OG), i.e. succinyl phosphonate (SP) and phosphono ethyl succinyl phosphonate (PESP), as tools to isolate the first catalytic steps and understand the significance of conformational transitions for the enzyme regulation. The kinetics showed a more efficient inhibition of mycobacterial E1o by SP (K i 0.043 ± 0.013 mM) than PESP (K i 0.88 ± 0.28 mM), consistent with the different circular dichroism spectra of the corresponding complexes. PESP allowed us to get crystallographic snapshots of the Michaelis-like complex, the first one for 2-oxo acid dehydrogenases, followed by the covalent adduction of the inhibitor to ThDP, mimicking the pre-decarboxylation complex. In addition, covalent ThDP-phosphonate complexes obtained with both compounds by co-crystallization were in the late conformational state, probably corresponding to slowly dissociating enzyme-inhibitor complexes. We discuss the relevance of these findings in terms of regulatory features of the mycobacterial E1o enzymes, and in the perspective of developing tools for species-specific metabolic regulation.


    Organizational Affiliation

    Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France. Electronic address: marco.bellinzoni@pasteur.fr.,A.N. Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia.,Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Multifunctional 2-oxoglutarate metabolism enzyme
A, B, C, D
868Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: kgd (sucA)
Find proteins for A0R2B1 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R2B1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, B, C, D
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
JQ5
Query on JQ5

Download SDF File 
Download CCD File 
A, B, C, D
4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanylidene-butanoic acid
C6 H11 O6 P
YEJCRQSMXRSGOQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.232 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 81.390α = 99.54
b = 83.960β = 98.78
c = 160.680γ = 100.89
Software Package:
Software NamePurpose
AutoPROCdata scaling
REFMACphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release