This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
3e3k
From Proteopedia
(Difference between revisions)
m (Protected "3e3k" [edit=sysop:move=sysop]) |
|||
| (5 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:3e3k.png|left|200px]] | ||
| - | + | ==Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form)== | |
| + | <StructureSection load='3e3k' size='340' side='right'caption='[[3e3k]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3e3k]] 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=3E3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E3K 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]] 2.8Å</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=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=3e3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e3k OCA], [https://pdbe.org/3e3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e3k RCSB], [https://www.ebi.ac.uk/pdbsum/3e3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e3k 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/e3/3e3k_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=3e3k 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 3e3k" 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]] | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form)
| |||||||||||
