2npd: Difference between revisions

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-[[Image:2npd.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2npd", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2npd|  PDB=2npd  |  SCENE=  }}
-'''An unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance'''
+==An unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance==
+<StructureSection load='2npd' size='340' side='right'caption='[[2npd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2npd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NPD 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]] 2.1&#8491;</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=IMD:IMIDAZOLE'>IMD</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=2npd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2npd OCA], [https://pdbe.org/2npd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2npd RCSB], [https://www.ebi.ac.uk/pdbsum/2npd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2npd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI] Involved in the uptake of ammonia.
+== 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/np/2npd_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=2npd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Amt proteins constitute a class of ubiquitous integral membrane proteins that mediate movement of ammonium across cell membranes. They are homotrimers, in which each subunit contains a narrow pore through which substrate transport occurs. Two conserved histidine residues in the pore have been proposed to be necessary for ammonia conductance. By analyzing 14 engineered polar and non-polar variants of these histidines, in Escherichia coli AmtB, we show that both histidines are absolutely required for optimum substrate conductance. Crystal structures of variants confirm that substitution of the histidine residues does not affect AmtB structure. In a subgroup of Amt proteins, found only in fungi, one of the histidines is replaced by glutamate. The equivalent substitution in E. coli AmtB is partially active, and the structure of this variant suggests that the glutamate side chain can make similar interactions to those made by histidine.
-==Overview==
+An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance.,Javelle A, Lupo D, Zheng L, Li XD, Winkler FK, Merrick M J Biol Chem. 2006 Dec 22;281(51):39492-8. Epub 2006 Oct 12. PMID:17040913<ref>PMID:17040913</ref>
-Amt proteins constitute a class of ubiquitous integral membrane proteins that mediate movement of ammonium across cell membranes. They are homotrimers, in which each subunit contains a narrow pore through which substrate transport occurs. Two conserved histidine residues in the pore have been proposed to be necessary for ammonia conductance. By analyzing 14 engineered polar and non-polar variants of these histidines, in Escherichia coli AmtB, we show that both histidines are absolutely required for optimum substrate conductance. Crystal structures of variants confirm that substitution of the histidine residues does not affect AmtB structure. In a subgroup of Amt proteins, found only in fungi, one of the histidines is replaced by glutamate. The equivalent substitution in E. coli AmtB is partially active, and the structure of this variant suggests that the glutamate side chain can make similar interactions to those made by histidine.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-NPD is a [[Single protein]] structure of 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=2NPD OCA].
+</div>
+<div class="pdbe-citations 2npd" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance., Javelle A, Lupo D, Zheng L, Li XD, Winkler FK, Merrick M, J Biol Chem. 2006 Dec 22;281(51):39492-8. Epub 2006 Oct 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17040913 17040913]
+*[[Ion channels 3D structures|Ion channels 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Lupo, D.]]
+[[Category: Lupo D]]
-[[Category: Winkler, F K.]]
+[[Category: Winkler FK]]
-[[Category: Ammonia transport]]
-[[Category: Amtb]]
-[[Category: Histidine mutant]]
-[[Category: Membrane protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 09:44:24 2008''