3ub7: Difference between revisions

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==Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with acetamide bound==
==Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with acetamide bound==
<StructureSection load='3ub7' size='340' side='right' caption='[[3ub7]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='3ub7' size='340' side='right'caption='[[3ub7]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ub7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori_ss1 Helicobacter pylori ss1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UB7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UB7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ub7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_SS1 Helicobacter pylori SS1]. The February 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Proton-Gated Urea Channel''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_2 10.2210/rcsb_pdb/mom_2013_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UB7 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACM:ACETAMIDE'>ACM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.4&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ub6|3ub6]], [[3ub8|3ub8]], [[3ub9|3ub9]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACM:ACETAMIDE'>ACM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3ub7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ub7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ub7 RCSB], [http://www.ebi.ac.uk/pdbsum/3ub7 PDBsum]</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=3ub7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ub7 OCA], [https://pdbe.org/3ub7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ub7 RCSB], [https://www.ebi.ac.uk/pdbsum/3ub7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ub7 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/B6JPK4_HELP2 B6JPK4_HELP2]
pH sensing is crucial for survival of most organisms, yet the molecular basis of such sensing is poorly understood. Here, we present an atomic resolution structure of the periplasmic portion of the acid-sensing chemoreceptor, TlpB, from the gastric pathogen Helicobacter pylori. The structure reveals a universal signaling fold, a PAS domain, with a molecule of urea bound with high affinity. Through biophysical, biochemical, and in vivo mutagenesis studies, we show that urea and the urea-binding site residues play critical roles in the ability of H. pylori to sense acid. Our signaling model predicts that protonation events at Asp114, affected by changes in pH, dictate the stability of TlpB through urea binding.
 
Structure and Proposed Mechanism for the pH-Sensing Helicobacter pylori Chemoreceptor TlpB.,Goers Sweeney E, Henderson JN, Goers J, Wreden C, Hicks KG, Foster JK, Parthasarathy R, Remington SJ, Guillemin K Structure. 2012 Jun 14. PMID:22705207<ref>PMID:22705207</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Helicobacter pylori ss1]]
[[Category: Helicobacter pylori SS1]]
[[Category: Goers, J]]
[[Category: Large Structures]]
[[Category: Guillemin, K J]]
[[Category: Proton-Gated Urea Channel]]
[[Category: Henderson, J N]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Hicks, K G]]
[[Category: Goers J]]
[[Category: Parthasarathy, R]]
[[Category: Guillemin KJ]]
[[Category: Remington, S J]]
[[Category: Henderson JN]]
[[Category: Sweeney, E G]]
[[Category: Hicks KG]]
[[Category: Wreden, C]]
[[Category: Parthasarathy R]]
[[Category: Four-helix bundle]]
[[Category: Remington SJ]]
[[Category: Homodimer]]
[[Category: Sweeney EG]]
[[Category: Membrane protein]]
[[Category: Wreden C]]
[[Category: Pas domain]]

Latest revision as of 13:19, 1 March 2024

Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with acetamide boundPeriplasmic portion of the Helicobacter pylori chemoreceptor TlpB with acetamide bound

Structural highlights

3ub7 is a 2 chain structure with sequence from Helicobacter pylori SS1. The February 2013 RCSB PDB Molecule of the Month feature on Proton-Gated Urea Channel by David Goodsell is 10.2210/rcsb_pdb/mom_2013_2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B6JPK4_HELP2

3ub7, resolution 1.40Å

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OCA
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