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==Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form)==
==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]] 2.80&Aring;' scene=''>
<StructureSection load='3e3k' size='340' side='right'caption='[[3e3k]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3e3k]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E3K FirstGlance]. <br>
<table><tr><td colspan='2'>[[3e3k]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. 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='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=SO4:SULFATE+ION'>SO4</scene></td></tr>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dp8|3dp8]], [[1zlq|1zlq]], [[1uiu|1uiu]], [[1uiv|1uiv]], [[2noo|2noo]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dp8|3dp8]], [[1zlq|1zlq]], [[1uiu|1uiu]], [[1uiv|1uiv]], [[2noo|2noo]]</div></td></tr>
<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=83333 ECOLI])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nikA, b3476, JW3441 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
<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=3e3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e3k OCA], [http://pdbe.org/3e3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e3k RCSB], [http://www.ebi.ac.uk/pdbsum/3e3k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e3k ProSAT]</span></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>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/NIKA_ECOLI NIKA_ECOLI]] Involved in a nickel transport system, probably represents the nickel binder.  
[[https://www.uniprot.org/uniprot/NIKA_ECOLI NIKA_ECOLI]] Involved in a nickel transport system, probably represents the nickel binder.  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</div>
</div>
<div class="pdbe-citations 3e3k" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 3e3k" style="background-color:#fffaf0;"></div>
==See Also==
*[[ABC transporter 3D structures|ABC transporter 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Ecoli]]
[[Category: Ecoli]]
[[Category: Large Structures]]
[[Category: Bochot, C]]
[[Category: Bochot, C]]
[[Category: Cavazza, C]]
[[Category: Cavazza, C]]

Revision as of 14:39, 16 February 2022

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form)Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form)

Structural highlights

3e3k is a 3 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , , ,
Gene:nikA, b3476, JW3441 (ECOLI)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NIKA_ECOLI] Involved in a nickel transport system, probably represents the nickel binder.

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

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[1]

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

See Also

References

  1. ↑ Cherrier MV, Cavazza C, Bochot C, Lemaire D, Fontecilla-Camps JC. Structural Characterization of a Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter NikA. Biochemistry. 2008 Sep 23;47(38):9937-9943. Epub 2008 Aug 30. PMID:18759453 doi:10.1021/bi801051y

3e3k, resolution 2.80Å

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OCA
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