2vyc: Difference between revisions

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-[[Image:2vyc.png|left|200px]]
-<!--
+==Crystal Structure of Acid Induced Arginine Decarboxylase from E. coli==
-The line below this paragraph, containing "STRUCTURE_2vyc", creates the "Structure Box" on the page.
+<StructureSection load='2vyc' size='340' side='right'caption='[[2vyc]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2vyc]] is a 10 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=2VYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VYC FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
--->
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Arginine_decarboxylase Arginine decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.19 4.1.1.19] </span></td></tr>
-{{STRUCTURE_2vyc|  PDB=2vyc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vyc OCA], [https://pdbe.org/2vyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vyc RCSB], [https://www.ebi.ac.uk/pdbsum/2vyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vyc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/ADIA_ECOLI ADIA_ECOLI]] ADC can be found in two forms: biodegradative and biosynthetic. The biodegradative form may play a role in regulating pH by consuming proteins.
+== 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/vy/2vyc_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=2vyc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The acid induced arginine decarboxylase is part of an enzymatic system in Escherichia coli that contributes to making this organism acid resistant. The arginine decarboxylase is a vitamin B6-dependent enzyme that is active at acidic pH. It consumes a proton in the decarboxylation of arginine to agmatine and by working in tandem with an arginine-agmatine antiporter this enzymatic cycle protects the organism by preventing the accumulation of protons inside the cell. We have determined the structure of the acid induced arginine decarboxylase by X-ray crystallography to 2.4 A resolution. The arginine decarboxylase structure, revealed a ca. 800 kDa decamer composed as a pentamer of five homodimers. Each homodimer has an abundance of acidic surface residues, which at neutral pH prevent inactive homodimers from associating into active decamers. Conversely, acidic conditions favor the assembly of active decamers. Therefore, the structure of arginine decarboxylase presents a mechanism by which its activity is modulated by external pH.
-===CRYSTAL STRUCTURE OF ACID INDUCED ARGININE DECARBOXYLASE FROM E. COLI===
+Crystal Structure of the Acid Induced Arginine Decarboxylase from Escherichia coli: Reversible Decamer Assembly Controls Enzyme Activity.,Andrell J, Hicks M, Palmer T, Carpenter E, Iwata S, Maher M Biochemistry. 2009 Mar 19. PMID:19298070<ref>PMID:19298070</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19298070}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vyc" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19298070 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19298070}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[2vyc]] is a 10 chain structure with 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=2VYC OCA].
-==Reference==
-<ref group="xtra">PMID:019298070</ref><references group="xtra"/>
 [[Category: Arginine decarboxylase]]
 [[Category: Escherichia coli]]
-[[Category: Andrell, J.]]
+[[Category: Large Structures]]
-[[Category: Carpenter, E P.]]
+[[Category: Andrell, J]]
-[[Category: Hicks, M G.]]
+[[Category: Carpenter, E P]]
-[[Category: Iwata, S.]]
+[[Category: Hicks, M G]]
-[[Category: Maher, M J.]]
+[[Category: Iwata, S]]
-[[Category: Palmer, T.]]
+[[Category: Maher, M J]]
+[[Category: Palmer, T]]
 [[Category: Acid resistance]]
-[[Category: Arginine decarboxylase]]
 [[Category: Decarboxylase]]
 [[Category: Lyase]]
 [[Category: Plp-dependent enzyme]]
 [[Category: Pyridoxal phosphate]]