6vst: Difference between revisions
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==Arginase from Medicago truncatula in complex with ornithine== | ==Arginase from Medicago truncatula in complex with ornithine== | ||
<StructureSection load='6vst' size='340' side='right'caption='[[6vst]]' scene=''> | <StructureSection load='6vst' size='340' side='right'caption='[[6vst]], [[Resolution|resolution]] 2.12Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VST OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VST FirstGlance]. <br> | <table><tr><td colspan='2'>[[6vst]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Barrel_medic Barrel medic]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VST OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VST FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vst FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vst OCA], [http://pdbe.org/6vst PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vst RCSB], [http://www.ebi.ac.uk/pdbsum/6vst PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vst ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">11420737, MTR_4g024960, MtrunA17_Chr4g0011501 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3880 Barrel medic])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vst FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vst OCA], [http://pdbe.org/6vst PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vst RCSB], [http://www.ebi.ac.uk/pdbsum/6vst PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vst ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Arginine acts as a precursor of polyamines in plants in two known pathways, agmatine and ornithine routes. It is decarboxylated to agmatine by arginine decarboxylase, and then transformed to putrescine by the consecutive action of agmatine iminohydrolase and N-carbamoylputrescine amidohydrolase. Alternatively, it can be hydrolyzed to ornithine by arginase and then decarboxylated by ornithine decarboxylase to putrescine. Some plants lack a functional ornithine pathway, but all have one or two arginases that can have dual cellular localization, in mitochondria and plastids. It was recently shown that arginases from Arabidopsis thaliana and soybean act also as agmatinases, thus they can produce putrescine directly from agmatine. Therefore, arginase (together with arginine decarboxylase) can complement putrescine production in plastids, providing a third polyamine biosynthesis pathway in plants. Phylogenetic analysis suggests that arginases, highly conserved in the plant kingdom, create the only group of enzymes recognized in the family of ureohydrolases in plants. Arginases are metalloenzymes with binuclear manganese cluster in the active site. In this work, two arginases from A. thaliana and Medicago truncatula are structurally characterized and their binding properties are discussed. Crystal structures with bound ornithine show that plant hexameric arginases engage a long loop from the neighboring subunit to stabilize alpha-amino and carboxyl groups of the ligand. This unique ligand binding mode is unobserved in arginases from other domains of life. Structural analysis shows that substrate binding by residues from two neighboring subunits might also characterize some prokaryotic agmatinases. This feature of plant arginases is most likely the determinant of their ability to recognize not only arginine but also agmatine as their substrates, thus, to act as arginase and agmatinase. | |||
The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases.,Sekula B Front Plant Sci. 2020 Jul 10;11:987. doi: 10.3389/fpls.2020.00987. eCollection, 2020. PMID:32754173<ref>PMID:32754173</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6vst" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Arginase]] | |||
[[Category: Barrel medic]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Sekula B]] | [[Category: Sekula, B]] | ||
[[Category: Agmatinase]] | |||
[[Category: Agmatine amidinohydrolase]] | |||
[[Category: Arginine amidinohydrolase]] | |||
[[Category: Hydrolase]] | |||
[[Category: Ureohydrolase]] | |||