PDBsum entry 6f4l

Transferase

PDB id: 6f4l

Contents

Protein chain

302 a.a.

Ligands

SF4

NTM

NHE

Metals

_CL

Waters ×38

PDB id:

6f4l

Name:

Transferase

Title:

Structure of quinolinate synthase with inhibitor-derived quinolinate

Structure:

Quinolinate synthase a. Chain: a. Engineered: yes. Mutation: yes

Source:

Thermotoga maritima (strain atcc 43589 / msb8 / dsm 3109 / jcm 10099). Organism_taxid: 243274. Strain: atcc 43589 / msb8 / dsm 3109 / jcm 10099. Gene: nada, tm_1644. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.30Å R-factor: 0.203 R-free: 0.220

Authors:

A.Volbeda,J.C.Fontecilla-Camps

Key ref:

A.Volbeda et al. (2018). Crystallographic Trapping of Reaction Intermediates in Quinolinic Acid Synthesis by NadA. ACS Chem Biol, 13, 1209-1217. PubMed id: 29641168 DOI: 10.1021/acschembio.7b01104

Date:

29-Nov-17 Release date: 25-Apr-18

Protein chain

Q9X1X7  (NADA_THEMA) -  Quinolinate synthase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 298 a.a.

Struc: 302 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.5.1.72 - quinolinate synthase.
• Reaction: iminosuccinate + dihydroxyacetone phosphate = quinolinate + phosphate + 2 H2O + H⁺

iminosuccinate + dihydroxyacetone phosphate = quinolinate + phosphate + 2 × H2O + H(+) (Bound ligand (Het Group name = NTM) corresponds exactly)

• Cofactor: Iron-sulfur

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/acschembio.7b01104

ACS Chem Biol 13:1209-1217 (2018)

PubMed id: 29641168

Crystallographic Trapping of Reaction Intermediates in Quinolinic Acid Synthesis by NadA.

A.Volbeda, J.Saez Cabodevilla, C.Darnault, O.Gigarel, T.H.Han, O.Renoux, O.Hamelin, S.Ollagnier-de-Choudens, P.Amara, J.C.Fontecilla-Camps.

ABSTRACT

NadA is a multifunctional enzyme that condenses dihydroxyacetone phosphate (DHAP) with iminoaspartate (IA) to generate quinolinic acid (QA), the universal precursor of the nicotinamide adenine dinucleotide (NAD(P)) cofactor. Using X-ray crystallography, we have (i) characterized two of the reaction intermediates of QA synthesis using a "pH-shift" approach and a slowly reacting Thermotoga maritima NadA variant and (ii) observed the QA product, resulting from the degradation of an intermediate analogue, bound close to the entrance of a long tunnel leading to the solvent medium. We have also used molecular docking to propose a condensation mechanism between DHAP and IA based on two previously published Pyrococcus horikoshi NadA structures. The combination of reported data and our new results provide a structure-based complete catalytic sequence of QA synthesis by NadA.