2BJ8

NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH and LOW-AFFINITY SITES

PDB DOI: https://doi.org/10.2210/pdb2BJ8/pdb

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

Deposited: 2005-01-31 Released: 2005-04-08
Deposition Author(s): Tahirov, T.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.229
R-Value Work: 0.200
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of Pyrococcus Horikoshii Nikr: Nickel Sensing and Implications for the Regulation of DNA Recognition

Chivers, P.T., Tahirov, T.H.

(2005) J Mol Biol 348: 597

PubMed: 15826657 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2005.03.017
Primary Citation of Related Structures:
2BJ1, 2BJ3, 2BJ7, 2BJ8, 2BJ9

PubMed Abstract:
The Pyrococcus horikoshii OT3 genome contains a gene (PH0601 or nikR) encoding a protein (PhNikR) that shares 33.8% amino acid sequence identity with Escherichia coli nickel responsive repressor NikR (EcNikR), including many residues that are functionally important in the E.coli ortholog. We succeeded in crystallization and structural characterization of PhNikR in the apo form and two nickel bound forms that exhibit different conformations, open and closed. Moreover, we have identified a putative "low-affinity" nickel-binding pocket in the closed form. This binding site has unusual nickel coordination and exhibits high sensitivity to phosphate in the crystal structure. Analysis of the PhNikR structures and structure-based mutational studies with EcNikR reveals a plausible mechanism of nickel-dependent promoter recognition by the NikR family of proteins.

Organizational Affiliation

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.

Macromolecule Content

Total Structure Weight: 32.54 kDa
Atom Count: 2,346
Modelled Residue Count: 275
Deposited Residue Count: 276
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NICKEL RESPONSIVE REGULATOR	A, B	138	Pyrococcus horikoshii OT3	Mutation(s): 0
UniProt
Find proteins for O58316 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58316 Go to UniProtKB: O58316
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O58316
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth B]	C [auth A] F [auth B] G [auth B] H [auth B] I [auth B] C [auth A], F [auth B], G [auth B], H [auth B], I [auth B], L [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]