PDBsum entry 4zk6

Transferase

PDB id: 4zk6

Contents

Protein chains

299 a.a.

Ligands

SF4-NTM ×2

ACT ×2

Metals

_NA ×4

_CL ×2

Waters ×287

PDB id:

4zk6

Name:

Transferase

Title:

Crystallographic capture of quinolinate synthase (nada) from pyrococcus horikoshii in its substrates and product-bound states

Structure:

Quinolinate synthase a. Chain: a, b. Engineered: yes

Source:

Pyrococcus horikoshii (strain atcc 700860 / dsm 12428 / jcm 9974 / nbrc 100139 / ot-3). Organism_taxid: 70601. Strain: atcc 700860 / dsm 12428 / jcm 9974 / nbrc 100139 / ot-3. Gene: nada, ph0013. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.90Å R-factor: 0.186 R-free: 0.231

Authors:

O.A.Esakova,T.L.Grove,A.H.Saunders,N.H.Yennawar,S.J.Booker

Key ref:

O.A.Esakova et al. (2016). Structure of Quinolinate Synthase from Pyrococcus horikoshii in the Presence of Its Product, Quinolinic Acid. J Am Chem Soc, 138, 7224-7227. PubMed id: 27224840 DOI: 10.1021/jacs.6b02708

Date:

29-Apr-15 Release date: 29-Jun-16

Protein chains

O57767  (NADA_PYRHO) -  Quinolinate synthase from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 300 a.a.

Struc: 299 a.a.

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/jacs.6b02708

J Am Chem Soc 138:7224-7227 (2016)

PubMed id: 27224840

Structure of Quinolinate Synthase from Pyrococcus horikoshii in the Presence of Its Product, Quinolinic Acid.

O.A.Esakova, A.Silakov, T.L.Grove, A.H.Saunders, M.I.McLaughlin, N.H.Yennawar, S.J.Booker.

ABSTRACT

Quinolinic acid (QA) is a common intermediate in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) 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 aspartate-enamine by the action of quinolinate synthase (NadA). NadA contains a [4Fe-4S] cluster cofactor with a unique, non-cysteinyl-ligated, iron ion (Fea), which is proposed to bind the hydroxyl group of a postulated intermediate in the last step of the reaction to facilitate a dehydration. However, direct evidence for this role in catalysis has yet to be provided. Herein, we present the structure of NadA in the presence of the product of its reaction, QA. We find that N1 and the C7 carboxylate group of QA ligate to Fea in a bidentate fashion, which is confirmed by Hyperfine Sublevel Correlation (HYSCORE) spectroscopy. This binding mode would place the C5 hydroxyl group of the postulated final intermediate distal to Fea and virtually incapable of coordinating to it. The structure shows that three strictly conserved amino acids, Glu198, Tyr109, and Tyr23, are in close proximity to the bound product. Substitution of these amino acids with Gln, Phe, and Phe, respectively, leads to complete loss of activity.