2k0q

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[[Image:2k0q.jpg|left|200px]]
 
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==Solution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34==
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The line below this paragraph, containing "STRUCTURE_2k0q", creates the "Structure Box" on the page.
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<StructureSection load='2k0q' size='340' side='right'caption='[[2k0q]]' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2k0q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_metallidurans_CH34 Cupriavidus metallidurans CH34]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K0Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K0Q FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2k0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k0q OCA], [https://pdbe.org/2k0q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k0q RCSB], [https://www.ebi.ac.uk/pdbsum/2k0q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k0q ProSAT]</span></td></tr>
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{{STRUCTURE_2k0q| PDB=2k0q | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/COPK_CUPMC COPK_CUPMC] Involved in resistance to copper. Can bind up to 2 copper ions. Has higher affinity for Cu(+) than for Cu(2+).<ref>PMID:18533181</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k0/2k0q_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2k0q ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans CH34 within the complex cop cluster of genes, for which 21 genes have been identified. The expression of the corresponding periplasmic CopK protein is strongly upregulated in the presence of copper, leading to a high periplasmic accumulation. The structure and metal-binding properties of CopK were investigated by NMR and mass spectrometry. The protein is dimeric in the apo state with a dissociation constant in the range of 10(-5) M estimated from analytical ultracentrifugation. Mass spectrometry revealed that CopK has two high-affinity Cu(I)-binding sites per monomer with different Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific. The solution structure of apo-CopK revealed an all-beta fold formed of two beta-sheets in perpendicular orientation with an unstructured C-terminal tail. The dimer interface is formed by the surface of the C-terminal beta-sheet. Binding of the first Cu(I)-ion induces a major structural modification involving dissociation of the dimeric apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm the conservation of the N-terminal beta-sheet, while the last strand of the C-terminal sheet appears in slow conformational exchange. We hypothesize that the partial disruption of the C-terminal beta-sheet is related to dimer dissociation. NH-exchange data acquired on the apo-protein are consistent with a lower thermodynamic stability of the C-terminal sheet. CopK contains seven methionine residues, five of which appear highly conserved. Chemical shift data suggest implication of two or three methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second Cu(I) ion further increases protein plasticity. Comparison of the structural and metal-binding properties of CopK with other periplasmic copper-binding proteins reveals two conserved features within these functionally related proteins: the all-beta fold and the methionine-rich Cu(I)-binding site.
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'''Solution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34'''
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Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge.,Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Coves J, Mergeay M, Wattiez R J Mol Biol. 2008 Jul 4;380(2):386-403. Epub 2008 May 15. PMID:18533181<ref>PMID:18533181</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==Overview==
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</div>
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The four replicons of Cupriavidus metallidurans CH34 (the genome sequence was provided by the US Department of Energy-University of California Joint Genome Institute) contain two gene clusters putatively encoding periplasmic resistance to copper, with an arrangement of genes resembling that of the copSRABCD locus on the 2.1 Mb megaplasmid (MPL) of Ralstonia solanacearum, a closely related plant pathogen. One of the copSRABCD clusters was located on the 2.6 Mb MPL, while the second was found on the pMOL30 (234 kb) plasmid as part of a larger group of genes involved in copper resistance, spanning 17 857 bp in total. In this region, 19 ORFs (copVTMKNSRABCDIJGFLQHE) were identified based on the sequencing of a fragment cloned in an IncW vector, on the preliminary annotation by the Joint Genome Institute, and by using transcriptomic and proteomic data. When introduced into plasmid-cured derivatives of C. metallidurans CH34, the cop locus was able to restore the wild-type MIC, albeit with a biphasic survival curve, with respect to applied Cu(II) concentration. Quantitative-PCR data showed that the 19 ORFs were induced from 2- to 1159-fold when cells were challenged with elevated Cu(II) concentrations. Microarray data showed that the genes that were most induced after a Cu(II) challenge of 0.1 mM belonged to the pMOL30 cop cluster. Megaplasmidic cop genes were also induced, but at a much lower level, with the exception of the highly expressed MPL copD. Proteomic data allowed direct observation on two-dimensional gel electrophoresis, and via mass spectrometry, of pMOL30 CopK, CopR, CopS, CopA, CopB and CopC proteins. Individual cop gene expression depended on both the Cu(II) concentration and the exposure time, suggesting a sequential scheme in the resistance process, involving genes such as copK and copT in an initial phase, while other genes, such as copH, seem to be involved in a late response phase. A concentration of 0.4 mM Cu(II) was the highest to induce maximal expression of most cop genes.
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<div class="pdbe-citations 2k0q" style="background-color:#fffaf0;"></div>
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== References ==
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==About this Structure==
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<references/>
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2K0Q is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Cupriavidus_metallidurans Cupriavidus metallidurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K0Q OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Cupriavidus metallidurans CH34]]
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Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34., Monchy S, Benotmane MA, Wattiez R, van Aelst S, Auquier V, Borremans B, Mergeay M, Taghavi S, van der Lelie D, Vallaeys T, Microbiology. 2006 Jun;152(Pt 6):1765-76. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16735739 16735739]
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[[Category: Large Structures]]
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[[Category: Cupriavidus metallidurans]]
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[[Category: Bersch B]]
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[[Category: Single protein]]
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[[Category: Coves J]]
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[[Category: Aelst, S van.]]
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[[Category: Favier A]]
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[[Category: Bersch, B.]]
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[[Category: Mergeay M]]
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[[Category: Coves, J.]]
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[[Category: Schanda P]]
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[[Category: Favier, A.]]
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[[Category: Vallaeys T]]
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[[Category: Mergeay, M.]]
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[[Category: Wattiez R]]
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[[Category: Schanda, P.]]
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[[Category: Van Aelst S]]
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[[Category: Vallaeys, T.]]
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[[Category: Wattiez, R.]]
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[[Category: Copper]]
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[[Category: Heavy metal resistance]]
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[[Category: Metal binding protein]]
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[[Category: Open barrel]]
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[[Category: Plasmid-encoded]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 28 09:12:14 2008''
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Current revision

Solution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34

PDB ID 2k0q

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