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| | ==Structure of H278A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate== | | ==Structure of H278A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate== |
| - | <StructureSection load='2aaf' size='340' side='right' caption='[[2aaf]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='2aaf' size='340' side='right'caption='[[2aaf]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2aaf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AAF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AAF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2aaf]] 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=2AAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AAF FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1rxx|1rxx]], [[2a9g|2a9g]], [[2abr|2abr]], [[2aci|2aci]]</td></tr>
| + | <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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">arcA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=2aaf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aaf OCA], [https://pdbe.org/2aaf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aaf RCSB], [https://www.ebi.ac.uk/pdbsum/2aaf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aaf ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </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=2aaf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aaf OCA], [http://pdbe.org/2aaf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aaf RCSB], [http://www.ebi.ac.uk/pdbsum/2aaf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2aaf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ARCA_PSEAE ARCA_PSEAE] |
| | == 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: Arginine deiminase]] | + | [[Category: Large Structures]] |
| - | [[Category: Dunaway-Mariano, D]] | + | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Galkin, A]] | + | [[Category: Dunaway-Mariano D]] |
| - | [[Category: Herzberg, O]] | + | [[Category: Galkin A]] |
| - | [[Category: Lu, X]] | + | [[Category: Herzberg O]] |
| - | [[Category: Arginine degradation pathway]]
| + | [[Category: Lu X]] |
| - | [[Category: Catalytic mechanism]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: L-arginine deiminase]]
| + | |
| Structural highlights
Function
ARCA_PSEAE
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
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Galkin A, Lu X, Dunaway-Mariano D, Herzberg O. Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase. J Biol Chem. 2005 Oct 7;280(40):34080-7. Epub 2005 Aug 9. PMID:16091358 doi:http://dx.doi.org/10.1074/jbc.M505471200
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