8P5R | pdb_00008p5r

Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.56 Å
  • R-Value Free: 
    0.229 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.

Yang, L.Wagner, T.Mechaly, A.Boyko, A.Bruch, E.M.Megrian, D.Gubellini, F.Alzari, P.M.Bellinzoni, M.

(2023) Nat Commun 14: 4851-4851

  • DOI: https://doi.org/10.1038/s41467-023-40253-6
  • Primary Citation Related Structures: 
    8P5R, 8P5S, 8P5T, 8P5U, 8P5V, 8P5W, 8P5X

  • PubMed Abstract: 

    Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI.


  • Organizational Affiliation
    • Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 1,488.09 kDa 
  • Atom Count: 57,005 
  • Modeled Residue Count: 7,346 
  • Deposited Residue Count: 13,448 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Multifunctional 2-oxoglutarate metabolism enzyme1,250Mycolicibacterium 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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycogen accumulation regulator GarA
G, H, I, J, K
G, H, I, J, K, L
158Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: garAMSMEG_3647MSMEI_3561
UniProt
Find proteins for A0QYG2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QYG2 
Go to UniProtKB:  A0QYG2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QYG2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
(Subject of Investigation/LOI)

Query on TPP



Download:Ideal Coordinates CCD File
AA [auth C]
DA [auth D]
GA [auth E]
JA [auth F]
S [auth A]
AA [auth C],
DA [auth D],
GA [auth E],
JA [auth F],
S [auth A],
W [auth B]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
CA

Query on CA



Download:Ideal Coordinates CCD File
CA [auth D]
FA [auth E]
IA [auth F]
R [auth A]
T [auth A]
CA [auth D],
FA [auth E],
IA [auth F],
R [auth A],
T [auth A],
V [auth B],
X [auth B],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
BA [auth D]
EA [auth E]
HA [auth F]
Q [auth A]
U [auth B]
BA [auth D],
EA [auth E],
HA [auth F],
Q [auth A],
U [auth B],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.56 Å
  • R-Value Free:  0.229 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 325.75α = 90
b = 325.75β = 90
c = 396.944γ = 120
Software Package:
Software NamePurpose
autoPROCdata processing
autoPROCdata processing
Aimlessdata scaling
autoPROCdata processing
BUSTERrefinement
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-13-JSV8-0003
Agence Nationale de la Recherche (ANR)FranceANR-18-CE92-0003

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Database references