2abr

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{{Seed}}
 
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[[Image:2abr.png|left|200px]]
 
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==Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate==
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The line below this paragraph, containing "STRUCTURE_2abr", creates the "Structure Box" on the page.
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<StructureSection load='2abr' size='340' side='right'caption='[[2abr]], [[Resolution|resolution]] 2.90&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'>[[2abr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ABR 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]] 2.9&#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=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</scene></td></tr>
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{{STRUCTURE_2abr| PDB=2abr | 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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [https://pdbe.org/2abr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [https://www.ebi.ac.uk/pdbsum/2abr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2abr ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ARCA_PSEAE ARCA_PSEAE]
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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/ab/2abr_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=2abr 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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L-arginine deiminase (ADI) catalyzes the irreversible hydrolysis of L-arginine to citrulline and ammonia. In a previous report of the structure of apoADI from Pseudomonas aeruginosa, the four residues that form the catalytic motif were identified as Cys406, His278, Asp280, and Asp166. The function of Cys406 in nucleophilic catalysis has been demonstrated by transient kinetic studies. In this study, the structure of the C406A mutant in complex with L-arginine is reported to provide a snapshot of the enzyme.substrate complex. Through the comparison of the structures of apoenzyme and substrate-bound enzyme, a substrate-induced conformational transition, which might play an important role in activity regulation, was discovered. Furthermore, the position of the guanidinium group of the bound substrate relative to the side chains of His278, Asp280, and Asp166 indicated that these residues mediate multiple proton transfers. His278 and Asp280, which are positioned to activate the water nucleophile in the hydrolysis of the S-alkylthiouronium intermediate, were replaced with alanine to stabilize the intermediate for structure determination. The structures determined for the H278A and D280A mutants co-crystallized with L-arginine provide a snapshot of the S-alkylthiouronium adduct formed by attack of Cys406 on the guanidinium carbon of L-arginine followed by the elimination of ammonia. Asp280 and Asp166 engage in ionic interactions with the guanidinium group in the C406A ADI. L-arginine structure and might orient the reaction center and participate in proton transfer. Structure determination of D166A revealed the apoD166A ADI. The collection of structures is interpreted in the context of recent biochemical data to propose a model for ADI substrate recognition and catalysis.
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===Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate===
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Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase.,Galkin A, Lu X, Dunaway-Mariano D, Herzberg O J Biol Chem. 2005 Oct 7;280(40):34080-7. Epub 2005 Aug 9. PMID:16091358<ref>PMID:16091358</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_16091358}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2abr" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 16091358 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16091358}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2ABR is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA].
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==Reference==
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<ref group="xtra">PMID:16091358</ref><references group="xtra"/>
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[[Category: Arginine deiminase]]
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[[Category: Pseudomonas aeruginosa]]
[[Category: Pseudomonas aeruginosa]]
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[[Category: Dunaway-Mariano, D.]]
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[[Category: Dunaway-Mariano D]]
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[[Category: Galkin, A.]]
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[[Category: Galkin A]]
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[[Category: Herzberg, O.]]
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[[Category: Herzberg O]]
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[[Category: Lu, X.]]
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[[Category: Lu X]]
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[[Category: Arginine degradation pathway]]
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[[Category: Catalytic mechanism]]
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[[Category: L-arginine deiminase]]
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[[Category: X-ray structure]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:40:24 2009''
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Current revision

Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate

PDB ID 2abr

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