3dp8

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[[Image:3dp8.png|left|200px]]
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==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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<StructureSection load='3dp8' size='340' side='right' caption='[[3dp8]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3dp8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DP8 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zlq|1zlq]], [[1uiu|1uiu]], [[1uiv|1uiv]], [[2noo|2noo]]</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nikA, b3476, JW3441 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dp8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dp8 RCSB], [http://www.ebi.ac.uk/pdbsum/3dp8 PDBsum]</span></td></tr>
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</table>
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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/dp/3dp8_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/chain_selection.php?pdb_ID=2ata 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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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.
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{{STRUCTURE_3dp8| PDB=3dp8 | SCENE= }}
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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>
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===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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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_18759453}}
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== References ==
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<references/>
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==About this Structure==
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__TOC__
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[[3dp8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DP8 OCA].
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</StructureSection>
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==Reference==
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<ref group="xtra">PMID:018759453</ref><references group="xtra"/>
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Bochot, C.]]
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[[Category: Bochot, C]]
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[[Category: Cavazza, C.]]
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[[Category: Cavazza, C]]
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[[Category: Cherrier, M V.]]
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[[Category: Cherrier, M V]]
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[[Category: Fontecilla-Camps, J C.]]
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[[Category: Fontecilla-Camps, J C]]
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[[Category: Lemaire, D.]]
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[[Category: Lemaire, D]]
[[Category: 4-tricarboxylate]]
[[Category: 4-tricarboxylate]]
[[Category: Butane-1]]
[[Category: Butane-1]]

Revision as of 08:16, 12 November 2014

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)

3dp8, resolution 2.50Å

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