6NSU

Crystallographic Capture of Quinolinate Synthase (NadA) from Pyrococcus horikoshii in its Substrates and Product-Bound States

Summary for 6NSU

• Entry DOI: 10.2210/pdb6nsu/pdb
• Related: 4ZK6 4ZKZ 5FEK 5FEU 5FEV 6NSO
• Descriptor: Quinolinate synthase A, IRON/SULFUR CLUSTER, DIDEHYDROASPARTATE, ... (4 entities in total)
• Functional Keywords: transferase
• Biological source: Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
• Total number of polymer chains: 1
• Total formula weight: 34672.75

Authors

Esakova, O.A.,Grove, T.L.,Silakov, A.,Yennawar, N.H.,Booker, S.J. (deposition date: 2019-01-25, release date: 2019-08-21, Last modification date: 2024-03-13)

Primary citation

Esakova, O.A.,Silakov, A.,Grove, T.L.,Warui, D.M.,Yennawar, N.H.,Booker, S.J.
An Unexpected Species Determined by X-ray Crystallography that May Represent an Intermediate in the Reaction Catalyzed by Quinolinate Synthase.
J.Am.Chem.Soc., 141:14142-14151, 2019

PubMed Abstract: Quinolinic acid is a common intermediate in the biosynthesis of nicotinamide adenine dinucleotide and its derivatives in all organisms that synthesize the molecule de novo. In most prokaryotes, it is formed from the condensation of dihydroxyacetone phosphate (DHAP) and iminoaspartate (IA) by the action of quinolinate synthase (NadA). NadA contains a [4Fe-4S] cluster cofactor with a unique noncysteinyl-ligated iron ion (Fe), which is proposed to bind the hydroxyl group of an intermediate in its reaction to facilitate a dehydration step. However, direct evidence for this role in catalysis has yet to be provided, and the exact chemical mechanism that underlies this transformation remains elusive. Herein, we present a structure of NadA from (PhNadA) in complex with IA and show that a carboxylate group of the molecule is ligated to Fe of the iron-sulfur cluster, occupying the site to which DHAP has been proposed to bind during catalysis. When crystals of PhNadA in complex with IA are soaked briefly in DHAP before freezing, electron density for a new molecule is observed, which we suggest is related to an intermediate in the reaction. Similar, but slightly different, "intermediates" are observed when crystals of a PhNadA Glu198Gln variant are incubated with DHAP, oxaloacetate, and ammonium chloride, conditions under which IA is formed chemically. Continuous-wave and pulse electron paramagnetic resonance techniques are used to verify the binding mode of substrates and proposed intermediates in frozen solution.

PubMed: 31390192
DOI: 10.1021/jacs.9b02513

Experimental method

X-RAY DIFFRACTION (2.15 Å)