7P4Q image
Entry Detail
PDB ID:
7P4Q
Keywords:
Title:
Structure of the quinolinate synthase S124A variant complexed with citrate
Biological Source:
PDB Version:
Deposition Date:
2021-07-12
Release Date:
2021-09-29
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.22
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Quinolinate synthase A
Chain IDs:A
Chain Length:305
Number of Molecules:1
Biological Source:Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
Primary Citation
Transient Formation of a Second Active Site Cavity during Quinolinic Acid Synthesis by NadA.
Acs Chem.Biol. 16 2423 2433 (2021)
PMID: 34609124 DOI: 10.1021/acschembio.1c00541

Abstact

Quinolinate synthase, also called NadA, is a [4Fe-4S]-containing enzyme that uses what is probably the oldest pathway to generate quinolinic acid (QA), the universal precursor of the biologically essential cofactor nicotinamide adenine dinucleotide (NAD). Its synthesis comprises the condensation of dihydroxyacetone phosphate (DHAP) and iminoaspartate (IA), which involves dephosphorylation, isomerization, cyclization, and two dehydration steps. The convergence of the three homologous domains of NadA defines a narrow active site that contains a catalytically essential [4Fe-4S] cluster. A tunnel, which can be opened or closed depending on the nature (or absence) of the bound ligand, connects this cofactor to the protein surface. One outstanding riddle has been the observation that the so far characterized active site is too small to bind IA and DHAP simultaneously. Here, we have used site-directed mutagenesis, X-ray crystallography, functional analyses, and molecular dynamics simulations to propose a condensation mechanism that involves the transient formation of a second active site cavity to which one of the substrates can migrate before this reaction takes place.

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