3c1j: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB== | ==Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB== | ||
<StructureSection load='3c1j' size='340' side='right' caption='[[3c1j]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='3c1j' size='340' side='right'caption='[[3c1j]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3c1j]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3c1j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C1J 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xqf|1xqf]], [[1u7g|1u7g]], [[2b2f|2b2f]], [[3b9w|3b9w]], [[3c1g|3c1g]], [[3c1h|3c1h]], [[3c1i|3c1i]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xqf|1xqf]], [[1u7g|1u7g]], [[2b2f|2b2f]], [[3b9w|3b9w]], [[3c1g|3c1g]], [[3c1h|3c1h]], [[3c1i|3c1i]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">1amtB ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">1amtB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1j OCA], [https://pdbe.org/3c1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c1j RCSB], [https://www.ebi.ac.uk/pdbsum/3c1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c1j ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI]] Involved in the uptake of ammonia. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c1/3c1j_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c1/3c1j_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 30: | Line 30: | ||
</div> | </div> | ||
<div class="pdbe-citations 3c1j" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3c1j" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Ion channels 3D structures|Ion channels 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 35: | Line 38: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus coli migula 1895]] | [[Category: Bacillus coli migula 1895]] | ||
[[Category: Large Structures]] | |||
[[Category: Lupo, D]] | [[Category: Lupo, D]] | ||
[[Category: Winkler, F K]] | [[Category: Winkler, F K]] | ||
| Line 42: | Line 46: | ||
[[Category: Membrane protein]] | [[Category: Membrane protein]] | ||
[[Category: Phe-gate double mutant]] | [[Category: Phe-gate double mutant]] | ||
[[Category: | [[Category: Transmembraneses']] | ||
[[Category: Transport protein]] | [[Category: Transport protein]] | ||
Revision as of 10:29, 10 November 2021
Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtBSubstrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB
Structural highlights
Function[AMTB_ECOLI] Involved in the uptake of ammonia. 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 PubMedThe conduction mechanism of Escherichia coli AmtB, the structurally and functionally best characterized representative of the ubiquitous Amt/Rh family, has remained controversial in several aspects. The predominant view has been that it facilitates the movement of ammonium in its uncharged form as indicated by the hydrophobic nature of a pore located in the center of each subunit of the homotrimer. Using site-directed mutagenesis and a combination of biochemical and crystallographic methods, we have investigated mechanistic questions concerning the putative periplasmic ammonium ion binding site S1 and the adjacent periplasmic "gate" formed by two highly conserved phenylalanine residues, F107 and F215. Our results challenge models that propose that NH(4)(+) deprotonation takes place at S1 before NH(3) conduction through the pore. The presence of S1 confers two critical features on AmtB, both essential for its function: ammonium scavenging efficiency at very low ammonium concentration and selectivity against water and physiologically important cations. We show that AmtB activity absolutely requires F215 but not F107 and that removal or obstruction of the phenylalanine gate produces an open but inactive channel. The phenyl ring of F215 must thus play a very specific role in promoting transfer and deprotonation of substrate from S1 to the central pore. We discuss these results with respect to three distinct mechanisms of conduction that have been considered so far. We conclude that substrate deprotonation is an essential part of the conduction mechanism, but we do not rule out net electrogenic transport. Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB.,Javelle A, Lupo D, Ripoche P, Fulford T, Merrick M, Winkler FK Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5040-5. Epub 2008 Mar 24. PMID:18362341[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
| ||||||||||||||||||||