2bj9

From Proteopedia

(Difference between revisions)

Current revision

NIKR with bound NICKEL and phosphate

Structural highlights

2bj9 is a 2 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

NIKR_PYRHO Transcriptional regulator (Potential).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Chivers PT, Tahirov TH. Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition. J Mol Biol. 2005 May 6;348(3):597-607. PMID:15826657 doi:http://dx.doi.org/10.1016/j.jmb.2005.03.017

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2bj9"

Categories: Large Structures | Pyrococcus horikoshii OT3 | Chivers PT | Tahirov TH

@@ Line 3: / Line 3: @@
 <StructureSection load='2bj9' size='340' side='right'caption='[[2bj9]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2bj9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BJ9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2bj9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BJ9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q5v|1q5v]], [[1q5y|1q5y]], [[2bj1|2bj1]], [[2bj3|2bj3]], [[2bj7|2bj7]], [[2bj8|2bj8]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bj9 OCA], [https://pdbe.org/2bj9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bj9 RCSB], [https://www.ebi.ac.uk/pdbsum/2bj9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bj9 ProSAT], [https://www.topsan.org/Proteins/RSGI/2bj9 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/NIKR_PYRHO NIKR_PYRHO]] Transcriptional regulator (Potential).
+[https://www.uniprot.org/uniprot/NIKR_PYRHO NIKR_PYRHO] Transcriptional regulator (Potential).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pyrococcus horikoshii]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Chivers, P T]]
+[[Category: Chivers PT]]
-[[Category: Tahirov, T H]]
+[[Category: Tahirov TH]]
-[[Category: Dna-binding]]
-[[Category: Metal-binding]]
-[[Category: Nickel]]
-[[Category: Nikr]]
-[[Category: Repressor]]
-[[Category: Structural genomic]]
-[[Category: Rsgi]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]

2bj9

From Proteopedia

Current revision

NIKR with bound NICKEL and phosphate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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