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7lol

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Current revision

The structure of Agmatinase from E. Coli at 1.8 A displaying urea and agmatine

Structural highlights

7lol is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7lol"

@@ Line 3: / Line 3: @@
 <StructureSection load='7lol' size='340' side='right'caption='[[7lol]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7lol]] is a 1 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=7LOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LOL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7lol]] is a 1 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=7LOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LOL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=URE:UREA'>URE</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]] 1.8&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=URE:UREA'>URE</scene></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=7lol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lol OCA], [https://pdbe.org/7lol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lol RCSB], [https://www.ebi.ac.uk/pdbsum/7lol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lol ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Agmatinase]]
 [[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]]

7lol

From Proteopedia

Current revision

The structure of Agmatinase from E. Coli at 1.8 A displaying urea and agmatine

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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