2bj8

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[[Image:2bj8.gif|left|200px]]<br /><applet load="2bj8" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:2bj8.gif|left|200px]]
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caption="2bj8, resolution 2.10&Aring;" />
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'''NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH AND LOW-AFFINITY SITES'''<br />
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{{Structure
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|PDB= 2bj8 |SIZE=350|CAPTION= <scene name='initialview01'>2bj8</scene>, resolution 2.10&Aring;
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|SITE= <scene name='pdbsite=AC1:Epe+Binding+Site+For+Chain+A'>AC1</scene>
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|LIGAND= <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene> and <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>
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|ACTIVITY=
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|GENE=
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}}
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'''NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH AND LOW-AFFINITY SITES'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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2BJ8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with <scene name='pdbligand=NI:'>NI</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=PG4:'>PG4</scene>, <scene name='pdbligand=EPE:'>EPE</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:Epe+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BJ8 OCA].
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2BJ8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BJ8 OCA].
==Reference==
==Reference==
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Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition., Chivers PT, Tahirov TH, J Mol Biol. 2005 May 6;348(3):597-607. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15826657 15826657]
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Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition., Chivers PT, Tahirov TH, J Mol Biol. 2005 May 6;348(3):597-607. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15826657 15826657]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
[[Category: Single protein]]
[[Category: Single protein]]
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[[Category: riken structural genomics/proteomics initiative]]
[[Category: riken structural genomics/proteomics initiative]]
[[Category: rsgi]]
[[Category: rsgi]]
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[[Category: structural genomics]]
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[[Category: structural genomic]]
[[Category: transcription]]
[[Category: transcription]]
[[Category: transcription regulation]]
[[Category: transcription regulation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:38:28 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:02:46 2008''

Revision as of 14:02, 20 March 2008

Image:2bj8.gif


PDB ID 2bj8

Drag the structure with the mouse to rotate
, resolution 2.10Å
Sites:
Ligands: , , , and
Coordinates: save as pdb, mmCIF, xml



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


Overview

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.

About this Structure

2BJ8 is a Single protein structure of sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA.

Reference

Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition., Chivers PT, Tahirov TH, J Mol Biol. 2005 May 6;348(3):597-607. PMID:15826657

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