5F3D

Structure of quinolinate synthase in complex with reaction intermediate W


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structures of Quinolinate Synthase in Complex with a Substrate Analogue, the Condensation Intermediate, and Substrate-Derived Product.

Volbeda, A.Darnault, C.Renoux, O.Reichmann, D.Amara, P.Ollagnier de Choudens, S.Fontecilla-Camps, J.C.

(2016) J.Am.Chem.Soc. 138: 11802-11809

  • DOI: 10.1021/jacs.6b05884
  • Primary Citation of Related Structures:  
  • Also Cited By: 6G74, 6F4L, 6F4D, 6F48

  • PubMed Abstract: 
  • The enzyme NadA catalyzes the synthesis of quinolinic acid (QA), the precursor of the universal nicotinamide adenine dinucleotide (NAD) cofactor. Here, we report the crystal structures of complexes between the Thermotoga maritima (Tm) NadA K219R/Y107 ...

    The enzyme NadA catalyzes the synthesis of quinolinic acid (QA), the precursor of the universal nicotinamide adenine dinucleotide (NAD) cofactor. Here, we report the crystal structures of complexes between the Thermotoga maritima (Tm) NadA K219R/Y107F variant and (i) the first intermediate (W) resulting from the condensation of dihydroxyacetone phosphate (DHAP) with iminoaspartate and (ii) the DHAP analogue and triose-phosphate isomerase inhibitor phosphoglycolohydroxamate (PGH). In addition, using the TmNadA K219R/Y21F variant, we have reacted substrates and obtained a crystalline complex between this protein and the QA product. We also show that citrate can bind to both TmNadA K219R and its Y21F variant. The W structure indicates that condensation causes dephosphorylation. We propose that catalysis by the K219R/Y107F variant is arrested at the W intermediate because the mutated protein is unable to catalyze its aldo-keto isomerization and/or cyclization that ultimately lead to QA formation. Intriguingly, PGH binds to NadA with its phosphate group at the site where the carboxylate groups of W also bind. Our results shed significant light on the mechanism of the reaction catalyzed by NadA.


    Related Citations: 
    • STRUCTURE OF THE FE4S4 QUINOLINATE SYNTHASE NADA FROM THERMOTOGA MARITIMA
      Cherrier, M.V.,Chan, A.,Darnaux, C.,Reichmann, D.,Amara, P.,Ollagnier de Choudens, S.,Fontecilla-Camps, J.C.
      (2014) J.AM.CHEM.SOC. 136: 5253


    Organizational Affiliation

    Metalloproteins Unit, Institut de Biologie Structurale, CEA, CNRS, Université Grenoble-Alpes , 71, Avenue des Martyrs, 38044 Grenoble Cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Quinolinate synthase A
A
305Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 2 
Gene Names: nadA
EC: 2.5.1.72
Find proteins for Q9X1X7 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X1X7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
5UK
Query on 5UK

Download SDF File 
Download CCD File 
A
2-IMINO,3-CARBOXY,5-OXO,6-HYDROXY HEXANOIC ACID
C7 H9 N O6
RVRAXUFLRLVVQJ-FMAAMLBYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.902α = 90.00
b = 49.029β = 105.40
c = 60.520γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-12-BS07-0018-01
French National Research AgencyFranceANR-11-LABX-0003-01

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references
  • Version 1.2: 2016-09-21
    Type: Database references
  • Version 1.3: 2017-08-16
    Type: Data collection
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence