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| | <StructureSection load='7lox' size='340' side='right'caption='[[7lox]], [[Resolution|resolution]] 3.20Å' scene=''> | | <StructureSection load='7lox' size='340' side='right'caption='[[7lox]], [[Resolution|resolution]] 3.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7lox]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LOX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7lox]] is a 3 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=7LOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LOX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7lol|7lol]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">speB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Agmatinase Agmatinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.11 3.5.3.11] </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=7lox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lox OCA], [https://pdbe.org/7lox PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lox RCSB], [https://www.ebi.ac.uk/pdbsum/7lox PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lox ProSAT]</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=7lox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lox OCA], [https://pdbe.org/7lox PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lox RCSB], [https://www.ebi.ac.uk/pdbsum/7lox PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lox ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/A0A4S5B4F2_ECOLI A0A4S5B4F2_ECOLI]] Catalyzes the formation of putrescine from agmatine.[HAMAP-Rule:MF_01418]
| + | [https://www.uniprot.org/uniprot/SPEB_ECOLI SPEB_ECOLI] Catalyzes the formation of putrescine from agmatine.<ref>PMID:10527864</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Agmatinase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Castro-Fernandez, V]] | + | [[Category: Castro-Fernandez V]] |
| - | [[Category: Figueroa, M]] | + | [[Category: Figueroa M]] |
| - | [[Category: Gonzalez-Ordenes, F]] | + | [[Category: Gonzalez-Ordenes F]] |
| - | [[Category: Martinez-Oyanedel, J]] | + | [[Category: Martinez-Oyanedel J]] |
| - | [[Category: Maturana, P]] | + | [[Category: Maturana P]] |
| - | [[Category: Uribe, E A]] | + | [[Category: Uribe EA]] |
| - | [[Category: Villalobos, P]] | + | [[Category: Villalobos P]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
SPEB_ECOLI Catalyzes the formation of putrescine from agmatine.[1]
Publication Abstract from PubMed
Agmatine is the product of the decarboxylation of L-arginine by the enzyme arginine decarboxylase. This amine has been attributed to neurotransmitter functions, anticonvulsant, anti-neurotoxic, and antidepressant in mammals and is a potential therapeutic agent for diseases such as Alzheimer's, Parkinson's, and cancer. Agmatinase enzyme hydrolyze agmatine into urea and putrescine, which belong to one of the pathways producing polyamines, essential for cell proliferation. Agmatinase from Escherichia coli (EcAGM) has been widely studied and kinetically characterized, described as highly specific for agmatine. In this study, we analyze the amino acids involved in the high specificity of EcAGM, performing a series of mutations in two loops critical to the active-site entrance. Two structures in different space groups were solved by X-ray crystallography, one at low resolution (3.2 A), including a guanidine group; and other at high resolution (1.8 A) which presents urea and agmatine in the active site. These structures made it possible to understand the interface interactions between subunits that allow the hexameric state and postulate a catalytic mechanism according to the Mn(2+) and urea/guanidine binding site. Molecular dynamics simulations evaluated the conformational dynamics of EcAGM and residues participating in non-binding interactions. Simulations showed the high dynamics of loops of the active site entrance and evidenced the relevance of Trp68, located in the adjacent subunit, to stabilize the amino group of agmatine by cation-pi interaction. These results allow to have a structural view of the best-kinetic characterized agmatinase in literature up to now.
Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity.,Maturana P, Orellana MS, Herrera SM, Martinez I, Figueroa M, Martinez-Oyanedel J, Castro-Fernandez V, Uribe E Int J Mol Sci. 2021 Apr 30;22(9). pii: ijms22094769. doi: 10.3390/ijms22094769. PMID:33946272[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Carvajal N, Olate J, Salas M, López V, Cerpa J, Herrera P, Uribe E. Evidence that histidine-163 is critical for catalytic activity, but not for substrate binding to Escherichia coli agmatinase. Biochem Biophys Res Commun. 1999 Oct 14;264(1):196-200. PMID:10527864 doi:10.1006/bbrc.1999.1505
- ↑ Maturana P, Orellana MS, Herrera SM, Martinez I, Figueroa M, Martinez-Oyanedel J, Castro-Fernandez V, Uribe E. Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity. Int J Mol Sci. 2021 Apr 30;22(9). pii: ijms22094769. doi: 10.3390/ijms22094769. PMID:33946272 doi:http://dx.doi.org/10.3390/ijms22094769
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