2jer

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{{Seed}}
 
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[[Image:2jer.png|left|200px]]
 
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==Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.==
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The line below this paragraph, containing "STRUCTURE_2jer", creates the "Structure Box" on the page.
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<StructureSection load='2jer' size='340' side='right'caption='[[2jer]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
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<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>
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{{STRUCTURE_2jer| PDB=2jer | SCENE= }}
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/AGUA_ENTFA AGUA_ENTFA]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/je/2jer_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2jer ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===AGMATINE DEIMINASE OF ENTEROCOCCUS FAECALIS CATALYZING ITS REACTION.===
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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<ref>PMID:17028272</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_17028272}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2jer" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 17028272 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17028272}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2JER is a 8 chains structure of sequences from [http://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].
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==Reference==
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<ref group="xtra">PMID:17028272</ref><references group="xtra"/>
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[[Category: Agmatine deiminase]]
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[[Category: Enterococcus faecalis]]
[[Category: Enterococcus faecalis]]
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[[Category: Llacer, J L.]]
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[[Category: Large Structures]]
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[[Category: Rubio, V.]]
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[[Category: Llacer JL]]
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[[Category: Tavarez, S.]]
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[[Category: Rubio V]]
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[[Category: 5- fold pseudosymmetric structure]]
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[[Category: Tavarez S]]
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[[Category: Agdi]]
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[[Category: Agmatine degradation pathway]]
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[[Category: Agmatine deiminase]]
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[[Category: Agmatine iminohydrolase]]
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[[Category: Covalent amidino adduct]]
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[[Category: Hydrolase]]
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[[Category: Tetramer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 10 18:23:23 2009''
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Current revision

Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.

PDB ID 2jer

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