2vyc: Difference between revisions
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The | ==Crystal Structure of Acid Induced Arginine Decarboxylase from E. coli== | ||
<StructureSection load='2vyc' size='340' side='right'caption='[[2vyc]], [[Resolution|resolution]] 2.40Å' scene=''> | |||
== Structural highlights == | |||
<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> | |||
</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> | |||
<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 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2vyc" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Arginine decarboxylase]] | |||
[[Category: Escherichia coli]] | |||
[[Category: Large Structures]] | |||
[[Category: Andrell, J]] | |||
[[Category: Carpenter, E P]] | |||
[[Category: Hicks, M G]] | |||
[[Category: Iwata, S]] | |||
[[Category: Maher, M J]] | |||
[[Category: Palmer, T]] | |||
[[Category: Acid resistance]] | |||
[[Category: Decarboxylase]] | |||
[[Category: Lyase]] | |||
[[Category: Plp-dependent enzyme]] | |||
[[Category: Pyridoxal phosphate]] | |||
Latest revision as of 14:49, 30 March 2022
Crystal Structure of Acid Induced Arginine Decarboxylase from E. coliCrystal Structure of Acid Induced Arginine Decarboxylase from E. coli
Structural highlights
Function[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 Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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