5F3D

Structure of quinolinate synthase in complex with reaction intermediate W

Summary for 5F3D

• Entry DOI: 10.2210/pdb5f3d/pdb
• Related: 4P3X
• Descriptor: Quinolinate synthase A, IRON/SULFUR CLUSTER, 2-IMINO,3-CARBOXY,5-OXO,6-HYDROXY HEXANOIC ACID, ... (5 entities in total)
• Functional Keywords: nad biosynthesis, iron sulfur cluster, transferase
• Biological source: Thermotoga maritima MSB8
• Cellular location: Cytoplasm : Q9X1X7
• Total number of polymer chains: 1
• Total formula weight: 35483.58

Authors

Volbeda, A.,Fontecilla-Camps, J.C. (deposition date: 2015-12-02, release date: 2016-08-31, Last modification date: 2024-01-10)

Primary citation

Volbeda, A.,Darnault, C.,Renoux, O.,Reichmann, D.,Amara, P.,Ollagnier de Choudens, S.,Fontecilla-Camps, J.C.
Crystal Structures of Quinolinate Synthase in Complex with a Substrate Analogue, the Condensation Intermediate, and Substrate-Derived Product.
J.Am.Chem.Soc., 138:11802-11809, 2016

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.

PubMed: 27545412
DOI: 10.1021/jacs.6b05884

Experimental method

X-RAY DIFFRACTION (1.9 Å)