6I0R | pdb_00006i0r

Structure of quinolinate synthase in complex with 5-mercaptopyridine-2,3-dicarboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb6I0R/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-10-26 Released: 2019-03-20 
• Deposition Author(s): Volbeda, A., Fontecilla-Camps, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.239 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Design of specific inhibitors of quinolinate synthase based on [4Fe-4S] cluster coordination.

Saez Cabodevilla, J., Volbeda, A., Hamelin, O., Latour, J.M., Gigarel, O., Clemancey, M., Darnault, C., Reichmann, D., Amara, P., Fontecilla-Camps, J.C., Ollagnier de Choudens, S.

(2019) Chem Commun (Camb) 55: 3725-3728

• PubMed: 30855610 
• DOI: https://doi.org/10.1039/c8cc09023h
• Primary Citation Related Structures: 
  6I0K, 6I0P, 6I0R


• PubMed Abstract: 
  

  Quinolinate synthase (NadA) is a [4Fe-4S] cluster-containing enzyme involved in the formation of quinolinic acid, the precursor of the essential NAD coenzyme. Here, we report the synthesis and activity of derivatives of the first inhibitor of NadA. Using multidisciplinary approaches we have investigated their action mechanism and discovered additional specific inhibitors of this enzyme.

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Organizational Affiliation: 
• Univ. Grenoble Alpes, CEA, CNRS, BIG-LCBM, UMR5249, 38000, Grenoble, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.2 kDa 
• Atom Count: 2,543 
• Modeled Residue Count: 303 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Quinolinate synthase A	A	305	Thermotoga maritima MSB8	Mutation(s): 2  Gene Names: nadA, TM_1644 EC: 2.5.1.72
UniProt
Find proteins for Q9X1X7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1X7  Go to UniProtKB:  Q9X1X7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QAT	J [auth A]	5-mercaptopyridine-2,3-dicarboxylic acid C7 H5 N O4 S XCYZNZIVHOIFRT-UHFFFAOYSA-N
FE	B [auth A], C [auth A], F [auth A], G [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
H2S	D [auth A], E [auth A], H [auth A], I [auth A]	HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.239 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.9	α = 90
b = 48.5	β = 107.1
c = 60.5	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Volbeda, A., Fontecilla-Camps, J.C.

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Funding Organization	Location	Grant Number
	France	ANR-16-CE18-0026

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description