5KTP | pdb_00005ktp

Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound itaconate and Fe4S4 cluster

• PDB DOI: https://doi.org/10.2210/pdb5KTP/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-12 Released: 2016-07-27 
• Deposition Author(s): Fenwick, M.K., Ealick, S.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of the Iron-Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate.

Fenwick, M.K., Ealick, S.E.

(2016) Biochemistry 55: 4135-4139

• PubMed: 27404889 
• DOI: https://doi.org/10.1021/acs.biochem.6b00626
• Primary Citation Related Structures: 
  5KTM, 5KTN, 5KTO, 5KTP, 5KTR, 5KTS, 5KTT


• PubMed Abstract: 
  

  The quinolinate synthase of prokaryotes and photosynthetic eukaryotes, NadA, contains a [4Fe-4S] cluster with unknown function. We report crystal structures of Pyrococcus horikoshii NadA in complex with dihydroxyacetone phosphate (DHAP), iminoaspartate analogues, and quinolinate. DHAP adopts a nearly planar conformation and chelates the [4Fe-4S] cluster via its keto and hydroxyl groups. The active site architecture suggests that the cluster acts as a Lewis acid in enediolate formation, like zinc in class II aldolases. The DHAP and putative iminoaspartate structures suggest a model for a condensed intermediate. The ensemble of structures suggests a two-state system, which may be exploited in early steps.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 35.12 kDa 
• Atom Count: 2,689 
• Modeled Residue Count: 297 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Quinolinate synthase A	A	304	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: nadA, PH0013 EC: 2.5.1.72
UniProt
Find proteins for O57767 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57767  Go to UniProtKB:  O57767

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
ITN	D [auth A]	2-methylidenebutanedioic acid C5 H6 O4 LVHBHZANLOWSRM-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NH4	E [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.477	α = 90
b = 52.671	β = 112.41
c = 55.686	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Fenwick, M.K., Ealick, S.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103403
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103485

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references
• Version 1.2: 2016-08-17
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence
• Version 1.5: 2023-10-04
  Changes: Data collection, Database references, Refinement description