5KTM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1021/acs.biochem.6b00626
  • Primary Citation of Related Structures:  

  • 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), iminoasparta ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Quinolinate synthase A
A
304Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Gene Names: nadA
EC: 2.5.1.72
Find proteins for O57767 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O57767
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.480α = 90.00
b = 52.877β = 111.72
c = 55.996γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103403
Department of Energy (United States)United StatesDE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103485

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2016-08-17
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations