5KTO

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

PDB DOI: https://doi.org/10.2210/pdb5KTO/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.189
R-Value Work: 0.140
R-Value Observed: 0.143

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 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

PubMed: 27404889 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.6b00626
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 35.45 kDa
Atom Count: 2,885
Modelled Residue Count: 298
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O57767
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NTM Query on NTM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	QUINOLINIC ACID C₇ H₅ N O₄ GJAWHXHKYYXBSV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.189
R-Value Work: 0.140
R-Value Observed: 0.143
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.9	α = 90
b = 52.424	β = 115.79
c = 55.313	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-07-27

Deposition Author(s):

Fenwick, M.K.

Ealick, S.E.

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 (Full details and data files)

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