4u4t: Difference between revisions

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 <StructureSection load='4u4t' size='340' side='right'caption='[[4u4t]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4u4t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_mg1655 Escherichia coli mg1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U4T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4u4t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U4T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4u4w|4u4w]], [[4u4v|4u4v]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">narK, b1223, JW1214 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511145 Escherichia coli MG1655])</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=4u4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u4t OCA], [https://pdbe.org/4u4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u4t RCSB], [https://www.ebi.ac.uk/pdbsum/4u4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u4t ProSAT]</span></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=4u4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u4t OCA], [http://pdbe.org/4u4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4u4t RCSB], [http://www.ebi.ac.uk/pdbsum/4u4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4u4t ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NARK_ECOLI NARK_ECOLI]] Involved in excretion of nitrite produced by the dissimilatory reduction of nitrate.
+[https://www.uniprot.org/uniprot/NARK_ECOLI NARK_ECOLI] Involved in excretion of nitrite produced by the dissimilatory reduction of nitrate.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-NarK belongs to the nitrate/nitrite porter (NNP) family in the major facilitator superfamily (MFS) and plays a central role in nitrate uptake across the membrane in diverse organisms, including archaea, bacteria, fungi and plants. Although previous studies provided insight into the overall structure and the substrate recognition of NarK, its molecular mechanism, including the driving force for nitrate transport, remained elusive. Here we demonstrate that NarK is a nitrate/nitrite antiporter, using an in vitro reconstituted system. Furthermore, we present the high-resolution crystal structures of NarK from Escherichia coli in the nitrate-bound occluded, nitrate-bound inward-open and apo inward-open states. The integrated structural, functional and computational analyses reveal the nitrate/nitrite antiport mechanism of NarK, in which substrate recognition is coupled to the transport cycle by the concomitant movement of the transmembrane helices and the key tyrosine and arginine residues in the substrate-binding site.
-Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK.,Fukuda M, Takeda H, Kato HE, Doki S, Ito K, Maturana AD, Ishitani R, Nureki O Nat Commun. 2015 May 11;6:7097. doi: 10.1038/ncomms8097. PMID:25959928<ref>PMID:25959928</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4u4t" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli mg1655]]
+[[Category: Escherichia coli str. K-12 substr. MG1655]]
 [[Category: Large Structures]]
-[[Category: Doki, S]]
+[[Category: Doki S]]
-[[Category: Fukuda, M]]
+[[Category: Fukuda M]]
-[[Category: Ishitani, R]]
+[[Category: Ishitani R]]
-[[Category: Ito, K]]
+[[Category: Ito K]]
-[[Category: Kato, H E]]
+[[Category: Kato HE]]
-[[Category: Maturana, A D]]
+[[Category: Maturana AD]]
-[[Category: Nureki, O]]
+[[Category: Nureki O]]
-[[Category: Takeda, H]]
+[[Category: Takeda H]]
-[[Category: Major facilitator superfamily]]
-[[Category: Membrane transporter]]
-[[Category: Nitrate nitrite porter family]]
-[[Category: Transport protein]]
-[[Category: Transporter]]