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3dp8
From Proteopedia
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| - | [[Image:3dp8.png|left|200px]] | ||
| - | + | ==Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)== | |
| + | <StructureSection load='3dp8' size='340' side='right'caption='[[3dp8]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3dp8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DP8 FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCT:(2R)-BUTANE-1,2,4-TRICARBOXYLIC+ACID'>HCT</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3dp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dp8 OCA], [https://pdbe.org/3dp8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dp8 RCSB], [https://www.ebi.ac.uk/pdbsum/3dp8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dp8 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/NIKA_ECOLI NIKA_ECOLI] Involved in a nickel transport system, probably represents the nickel binder. | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dp8_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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=3dp8 ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Escherichia coli and related bacteria require nickel for the synthesis of hydrogenases, enzymes involved in hydrogen oxidation and proton reduction. Nickel transport to the cytoplasm depends on five proteins, NikA-E. We have previously reported the three-dimensional structure of the soluble periplasmic nickel transporter NikA in a complex with FeEDTA(H 2O) (-). We have now determined the structure of EDTA-free NikA and have found that it binds a small organic molecule that contributes three ligands to the coordination of a transition metal ion. Unexpectedly, His416, which was far from the metal-binding site in the FeEDTA(H 2O) (-)-NikA complex, becomes the fourth observed ligand to the metal. The best match to the omit map electron density is obtained for butane-1,2,4-tricarboxylate (BTC). Our attempts to obtain a BTC-Ni-NikA complex using apo protein and commercial reagents resulted in nickel-free BTC-NikA. Overall, our results suggest that nickel transport in vivo requires a specific metallophore that may be BTC. | ||
| - | + | Structural Characterization of a Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter NikA.,Cherrier MV, Cavazza C, Bochot C, Lemaire D, Fontecilla-Camps JC Biochemistry. 2008 Sep 23;47(38):9937-9943. Epub 2008 Aug 30. PMID:18759453<ref>PMID:18759453</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 3dp8" style="background-color:#fffaf0;"></div> | ||
| - | == | + | ==See Also== |
| - | [[ | + | *[[ABC transporter 3D structures|ABC transporter 3D structures]] |
| - | + | == References == | |
| - | == | + | <references/> |
| - | < | + | __TOC__ |
| - | [[Category: Escherichia coli]] | + | </StructureSection> |
| - | [[Category: Bochot | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Cavazza | + | [[Category: Large Structures]] |
| - | [[Category: Cherrier | + | [[Category: Bochot C]] |
| - | [[Category: Fontecilla-Camps | + | [[Category: Cavazza C]] |
| - | [[Category: Lemaire | + | [[Category: Cherrier MV]] |
| - | + | [[Category: Fontecilla-Camps JC]] | |
| - | + | [[Category: Lemaire D]] | |
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Current revision
Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)
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