This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4exo

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:11, 14 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
==Revised, rerefined crystal structure of PDB entry 2QHK, methyl accepting chemotaxis protein==
==Revised, rerefined crystal structure of PDB entry 2QHK, methyl accepting chemotaxis protein==
-
<StructureSection load='4exo' size='340' side='right' caption='[[4exo]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+
<StructureSection load='4exo' size='340' side='right'caption='[[4exo]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4exo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"oceanomonas_parahaemolytica"_(fujino_et_al._1951)_miyamoto_et_al._1961 "oceanomonas parahaemolytica" (fujino et al. 1951) miyamoto et al. 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EXO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EXO FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4exo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_parahaemolyticus Vibrio parahaemolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EXO FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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]] 1.9&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qhk|2qhk]]</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=4exo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4exo OCA], [https://pdbe.org/4exo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4exo RCSB], [https://www.ebi.ac.uk/pdbsum/4exo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4exo ProSAT]</span></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GI:28896957, VP0183 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=670 "Oceanomonas parahaemolytica" (Fujino et al. 1951) Miyamoto et al. 1961])</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=4exo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4exo OCA], [http://pdbe.org/4exo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4exo RCSB], [http://www.ebi.ac.uk/pdbsum/4exo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4exo ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q87T87_VIBPA Q87T87_VIBPA]
-
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>
+
-
<div class="pdbe-citations 4exo" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
-
*[[Chemotaxis protein|Chemotaxis protein]]
+
*[[Chemotaxis protein 3D structures|Chemotaxis protein 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Foster, J K]]
+
[[Category: Large Structures]]
-
[[Category: Goers, J]]
+
[[Category: Vibrio parahaemolyticus]]
-
[[Category: Guillemin, K]]
+
[[Category: Foster JK]]
-
[[Category: Henderson, J N]]
+
[[Category: Goers J]]
-
[[Category: Hicks, K G]]
+
[[Category: Guillemin K]]
-
[[Category: Parthasarathy, R]]
+
[[Category: Henderson JN]]
-
[[Category: Remington, S J]]
+
[[Category: Hicks KG]]
-
[[Category: Sweeney, E G]]
+
[[Category: Parthasarathy R]]
-
[[Category: Wreden, C]]
+
[[Category: Remington SJ]]
-
[[Category: Chemotaxis receptor]]
+
[[Category: Sweeney EG]]
-
[[Category: Four helix bundle]]
+
[[Category: Wreden C]]
-
[[Category: Methyl accepting chemotaxis receptor]]
+
-
[[Category: Pas domain]]
+
-
[[Category: Periplasmic domain]]
+
-
[[Category: Signaling protein]]
+

Current revision

Revised, rerefined crystal structure of PDB entry 2QHK, methyl accepting chemotaxis protein

PDB ID 4exo

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4exo"
Personal tools