6R29

Crystal structure of the SucA domain of Mycobacterium smegmatis KGD cocrystallized with succinylphosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

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Ligand Structure Quality Assessment 


This is version 1.1 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 208: 182-190

  • DOI: 10.1016/j.jsb.2019.08.012
  • Primary Citation of Related Structures:  
    6R29, 6R2A, 6R2B, 6R2C, 6R2D

  • 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, previously named as the early and late state ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multifunctional 2-oxoglutarate metabolism enzymeA, B868Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: kgdsucAMSMEG_5049MSMEI_4922
EC: 2.2.1.5 (PDB Primary Data), 4.1.1.71 (PDB Primary Data), 1.2.4.2 (PDB Primary Data), 2.3.1.61 (PDB Primary Data)
UniProt
Find proteins for A0R2B1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R2B1 
Go to UniProtKB:  A0R2B1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R2B1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QSP
Query on QSP

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
(4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-oxidanyl-4-phosphono-butanoic acid
C16 H27 N4 O13 P3 S
XWZWGSGHSWWOAH-CVEARBPZSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.47α = 90
b = 108.17β = 103.78
c = 120.54γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references