4P3X

Structure of the Fe4S4 quinolinate synthase NadA from Thermotoga maritima

Summary for 4P3X

• Entry DOI: 10.2210/pdb4p3x/pdb
• Related: 1WZU 4HHE
• Descriptor: Quinolinate synthase A, IRON/SULFUR CLUSTER, ZINC ION, ... (5 entities in total)
• Functional Keywords: holo-protein, nad biosynthesis, catalytic triad, iron sulfur cluster, transferase
• Biological source: Thermotoga maritima
• Cellular location: Cytoplasm : Q9X1X7
• Total number of polymer chains: 1
• Total formula weight: 35309.99

Authors

Cherrier, M.V.,Chan, A.,Darnault, C.,Reichmann, D.,Amara, P.,Ollagnier de Choudens, S.,Fontecilla-Camps, J.C. (deposition date: 2014-03-10, release date: 2014-04-02, Last modification date: 2023-09-27)

Primary citation

Cherrier, M.V.,Chan, A.,Darnault, C.,Reichmann, D.,Amara, P.,Ollagnier de Choudens, S.,Fontecilla-Camps, J.C.
The crystal structure of Fe4S4 quinolinate synthase unravels an enzymatic dehydration mechanism that uses tyrosine and a hydrolase-type triad.
J.Am.Chem.Soc., 136:5253-5256, 2014

PubMed Abstract: Quinolinate synthase (NadA) is a Fe4S4 cluster-containing dehydrating enzyme involved in the synthesis of quinolinic acid (QA), the universal precursor of the essential nicotinamide adenine dinucleotide (NAD) coenzyme. A previously determined apo NadA crystal structure revealed the binding of one substrate analog, providing partial mechanistic information. Here, we report on the holo X-ray structure of NadA. The presence of the Fe4S4 cluster generates an internal tunnel and a cavity in which we have docked the last precursor to be dehydrated to form QA. We find that the only suitably placed residue to initiate this process is the conserved Tyr21. Furthermore, Tyr21 is close to a conserved Thr-His-Glu triad reminiscent of those found in proteases and other hydrolases. Our mutagenesis data show that all of these residues are essential for activity and strongly suggest that Tyr21 deprotonation, to form the reactive nucleophilic phenoxide anion, is mediated by the triad. NadA displays a dehydration mechanism significantly different from the one found in archetypical dehydratases such as aconitase, which use a serine residue deprotonated by an oxyanion hole. The X-ray structure of NadA will help us unveil its catalytic mechanism, the last step in the understanding of NAD biosynthesis.

PubMed: 24650327
DOI: 10.1021/ja501431b

Experimental method

X-RAY DIFFRACTION (1.65 Å)