5F3D

Structure of quinolinate synthase in complex with reaction intermediate W


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1021/jacs.6b05884
  • Primary Citation of Related Structures:  
    5F33, 5F35, 5F3D, 5LQM, 5LQS

  • 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/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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Quinolinate synthase A305Thermotoga maritima MSB8Mutation(s): 2 
Gene Names: nadATM_1644
EC: 2.5.1.72
UniProt
Find proteins for Q9X1X7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1X7 
Go to UniProtKB:  Q9X1X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1X7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.902α = 90
b = 49.029β = 105.4
c = 60.52γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2016-09-21
    Changes: Database references
  • Version 1.3: 2017-08-16
    Changes: Data collection
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Refinement description