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| | ==Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.== | | ==Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.== |
| - | <StructureSection load='2jer' size='340' side='right' caption='[[2jer]], [[Resolution|resolution]] 1.65Å' scene=''> | + | <StructureSection load='2jer' size='340' side='right'caption='[[2jer]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JER FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JER FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</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]] 1.65Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2j2t|2j2t]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [https://pdbe.org/2jer PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [https://www.ebi.ac.uk/pdbsum/2jer PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jer ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://pdbe.org/2jer PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jer ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/AGUA_ENTFA AGUA_ENTFA] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]] | + | [[Category: Enterococcus faecalis]] |
| - | [[Category: Agmatine deiminase]] | + | [[Category: Large Structures]] |
| - | [[Category: Llacer, J L]] | + | [[Category: Llacer JL]] |
| - | [[Category: Rubio, V]] | + | [[Category: Rubio V]] |
| - | [[Category: Tavarez, S]] | + | [[Category: Tavarez S]] |
| - | [[Category: 5- fold pseudosymmetric structure]]
| + | |
| - | [[Category: Agdi]]
| + | |
| - | [[Category: Agmatine degradation pathway]]
| + | |
| - | [[Category: Agmatine iminohydrolase]]
| + | |
| - | [[Category: Covalent amidino adduct]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Tetramer]]
| + | |
| Structural highlights
Function
AGUA_ENTFA
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 PubMed
Enterococcus faecalis makes ATP from agmatine in three steps catalyzed by agmatine deiminase (AgDI), putrescine transcarbamylase (PTC), and carbamate kinase (CK). An antiporter exchanges putrescine for agmatine. We have cloned the E. faecalis ef0732 and ef0734 genes of the reported gene cluster for agmatine catabolism, overexpressed them in Escherichia coli, purified the products, characterized them functionally as PTC and AgDI, and crystallized and X-ray diffracted them. The 1.65-Angstroms-resolution structure of AgDI forming a covalent adduct with an agmatine-derived amidine reactional intermediate is described. We provide definitive identification of the gene cluster for agmatine catabolism and confirm that ornithine is a genuine but poor PTC substrate, suggesting that PTC (found here to be trimeric) evolved from ornithine transcarbamylase. N-(Phosphonoacetyl)-putrescine was prepared and shown to strongly (K(i) = 10 nM) and selectively inhibit PTC and to improve PTC crystallization. We find that E. faecalis AgDI, which is committed to ATP generation, closely resembles the AgDIs involved in making polyamines, suggesting the recruitment of a polyamine-synthesizing AgDI into the AgDI pathway. The arginine deiminase (ADI) pathway of arginine catabolism probably supplied the genes for PTC and CK but not those for the agmatine/putrescine antiporter, and thus the AgDI and ADI pathways are not related by a single "en bloc" duplication event. The AgDI crystal structure reveals a tetramer with a five-blade propeller subunit fold, proves that AgDI closely resembles ADI despite a lack of sequence identity, and explains substrate affinity, selectivity, and Cys357-mediated-covalent catalysis. A three-tongued agmatine-triggered gating opens or blocks access to the active center.
The gene cluster for agmatine catabolism of Enterococcus faecalis: study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction.,Llacer JL, Polo LM, Tavarez S, Alarcon B, Hilario R, Rubio V J Bacteriol. 2007 Feb;189(4):1254-65. Epub 2006 Oct 6. PMID:17028272[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Llacer JL, Polo LM, Tavarez S, Alarcon B, Hilario R, Rubio V. The gene cluster for agmatine catabolism of Enterococcus faecalis: study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction. J Bacteriol. 2007 Feb;189(4):1254-65. Epub 2006 Oct 6. PMID:17028272 doi:10.1128/JB.01216-06
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