2BJ1

NIKR IN OPEN CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES

Summary for 2BJ1

• Entry DOI: 10.2210/pdb2bj1/pdb
• Related: 1Q5V 1Q5Y 2BJ3
• Descriptor: NICKEL RESPONSIVE REGULATOR, NICKEL (II) ION, CHLORIDE ION (3 entities in total)
• Functional Keywords: transcription, repressor, pyrococcus horikoshii, nikr, dna-binding, metal-binding, nickel, transcription regulation, riken structural genomics/proteomics initiative, rsgi, structural genomics
• Biological source: PYROCOCCUS HORIKOSHII
• Total number of polymer chains: 2
• Total formula weight: 31930.87

Authors

Tahirov, T.H. (deposition date: 2005-01-27, release date: 2005-04-08, Last modification date: 2023-12-13)

Primary citation

Chivers, P.T.,Tahirov, T.H.
Structure of Pyrococcus Horikoshii Nikr: Nickel Sensing and Implications for the Regulation of DNA Recognition
J.Mol.Biol., 348:597-, 2005

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.

PubMed: 15826657
DOI: 10.1016/J.JMB.2005.03.017

Experimental method

X-RAY DIFFRACTION (3 Å)