1v9y: Difference between revisions

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-[[Image:1v9y.png|left|200px]]
-{{STRUCTURE_1v9y|  PDB=1v9y  |  SCENE=  }}
+==Crystal Structure of the heme PAS sensor domain of Ec DOS (ferric form)==
+<StructureSection load='1v9y' size='340' side='right'caption='[[1v9y]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1v9y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9Y 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]] 1.32&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1v9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9y OCA], [https://pdbe.org/1v9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9y RCSB], [https://www.ebi.ac.uk/pdbsum/1v9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9y ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DOSP_ECOLI DOSP_ECOLI] Heme-based oxygen sensor protein displaying phosphodiesterase (PDE) activity toward c-di-GMP in response to oxygen availability. Involved in the modulation of intracellular c-di-GMP levels, in association with DosC which catalyzes the biosynthesis of c-di-GMP (diguanylate cyclase activity). Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria. Has very poor PDE activity on cAMP (PubMed:15995192) but is not active with cGMP, bis(p-nitrophenyl) phosphate or p-nitrophenyl phosphate (PubMed:11970957). Via its PDE activity on c-di-GMP, DosP regulates biofilm formation through the repression of transcription of the csgBAC operon, which encodes curli structural subunits.<ref>PMID:20553324</ref>
+== 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/v9/1v9y_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=1v9y ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+PAS domains, which have been identified in over 1100 proteins from all three kingdoms of life, convert various input stimuli into signals that propagate to downstream components by modifying protein-protein interactions. One such protein is the Escherichia coli redox sensor, Ec DOS, a phosphodiesterase that degrades cyclic adenosine monophosphate in a redox-dependent manner. Here we report the crystal structures of the heme PAS domain of Ec DOS in both inactive Fe(3+) and active Fe(2+) forms at 1.32 and 1.9 A resolution, respectively. The protein folds into a characteristic PAS domain structure and forms a homodimer. In the Fe(3+) form, the heme iron is ligated to a His-77 side chain and a water molecule. Heme iron reduction is accompanied by heme-ligand switching from the water molecule to a side chain of Met-95 from the FG loop. Concomitantly, the flexible FG loop is significantly rigidified, along with a change in the hydrogen bonding pattern and rotation of subunits relative to each other. The present data led us to propose a novel redox-regulated molecular switch in which local heme-ligand switching may trigger a global "scissor-type" subunit movement that facilitates catalytic control.
-===Crystal Structure of the heme PAS sensor domain of Ec DOS (ferric form)===
+A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor.,Kurokawa H, Lee DS, Watanabe M, Sagami I, Mikami B, Raman CS, Shimizu T J Biol Chem. 2004 May 7;279(19):20186-93. Epub 2004 Feb 23. PMID:14982921<ref>PMID:14982921</ref>
-{{ABSTRACT_PUBMED_14982921}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1v9y" style="background-color:#fffaf0;"></div>
-[[1v9y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9Y OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:014982921</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Escherichia coli k-12]]
+[[Category: Escherichia coli K-12]]
-[[Category: Kurokawa, H.]]
+[[Category: Large Structures]]
-[[Category: Lee, D S.]]
+[[Category: Kurokawa H]]
-[[Category: Mikami, B.]]
+[[Category: Lee DS]]
-[[Category: Raman, C S.]]
+[[Category: Mikami B]]
-[[Category: Sagami, I.]]
+[[Category: Raman CS]]
-[[Category: Shimizu, T.]]
+[[Category: Sagami I]]
-[[Category: Watanabe, M.]]
+[[Category: Shimizu T]]
-[[Category: Heme]]
+[[Category: Watanabe M]]
-[[Category: Pa]]
-[[Category: Sensor]]
-[[Category: Signaling protein]]