2nwl: Difference between revisions

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-{{Seed}}
-[[Image:2nwl.png|left|200px]]
-<!--
+==Crystal structure of GltPh in complex with L-Asp==
-The line below this paragraph, containing "STRUCTURE_2nwl", creates the "Structure Box" on the page.
+<StructureSection load='2nwl' size='340' side='right'caption='[[2nwl]], [[Resolution|resolution]] 2.96&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2nwl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NWL FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.96&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
-{{STRUCTURE_2nwl|  PDB=2nwl  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nwl OCA], [https://pdbe.org/2nwl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nwl RCSB], [https://www.ebi.ac.uk/pdbsum/2nwl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nwl ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLT_PYRHO GLT_PYRHO] Sodium-dependent, high-affinity amino acid transporter that mediates aspartate uptake (PubMed:17435767, PubMed:19380583, PubMed:17230192, Ref.11). Has only very low glutamate transport activity (PubMed:19380583, PubMed:17230192). Functions as a symporter that transports one amino acid molecule together with two or three Na(+) ions, resulting in electrogenic transport (PubMed:17435767, PubMed:19380583, Ref.11). Na(+) binding enhances the affinity for aspartate (PubMed:19380583, Ref.11). Mediates Cl(-) flux that is not coupled to amino acid transport; this avoids the accumulation of negative charges due to aspartate and Na(+) symport (PubMed:17435767). In contrast to mammalian homologs, transport does not depend on pH or K(+) ions (PubMed:19380583).<ref>PMID:17230192</ref> <ref>PMID:17435767</ref> <ref>PMID:19380583</ref> [PDB:4P19]
+== 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/nw/2nwl_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=2nwl ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Secondary transporters are integral membrane proteins that catalyse the movement of substrate molecules across the lipid bilayer by coupling substrate transport to one or more ion gradients, thereby providing a mechanism for the concentrative uptake of substrates. Here we describe crystallographic and thermodynamic studies of Glt(Ph), a sodium (Na+)-coupled aspartate transporter, defining sites for aspartate, two sodium ions and d,l-threo-beta-benzyloxyaspartate, an inhibitor. We further show that helical hairpin 2 is the extracellular gate that controls access of substrate and ions to the internal binding sites. At least two sodium ions bind in close proximity to the substrate and these sodium-binding sites, together with the sodium-binding sites in another sodium-coupled transporter, LeuT, define an unwound alpha-helix as the central element of the ion-binding motif, a motif well suited to the binding of sodium and to participation in conformational changes that accompany ion binding and unbinding during the transport cycle.
-===Crystal structure of GltPh in complex with L-Asp===
+Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter.,Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E Nature. 2007 Jan 25;445(7126):387-93. Epub 2007 Jan 17. PMID:17230192<ref>PMID:17230192</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2nwl" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17230192}}, adds the Publication Abstract to the page
+*[[Symporter 3D structures|Symporter 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17230192 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17230192}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-NWL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NWL OCA].
-==Reference==
-Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter., Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E, Nature. 2007 Jan 25;445(7126):387-93. Epub 2007 Jan 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17230192 17230192]
 [[Category: Pyrococcus horikoshii]]
-[[Category: Single protein]]
+[[Category: Boudker O]]
-[[Category: Boudker, O.]]
+[[Category: Gouaux E]]
-[[Category: Gouaux, E.]]
+[[Category: Ryan R]]
-[[Category: Ryan, R.]]
+[[Category: Shimamoto K]]
-[[Category: Shimamoto, K.]]
+[[Category: Yernool D]]
-[[Category: Yernool, D.]]
-[[Category: Alpha helical]]
-[[Category: Helical hairpin]]
-[[Category: Membrane protein]]
-[[Category: Unwound region]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 15:20:07 2008''