3rhy

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<StructureSection load='3rhy' size='340' side='right'caption='[[3rhy]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
<StructureSection load='3rhy' size='340' side='right'caption='[[3rhy]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3rhy]] is a 2 chain structure with sequence from [https://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=3RHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RHY FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3rhy]] is a 2 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=3RHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RHY FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HM3:(4-CHLOROPYRIDIN-2-YL)METHANOL'>HM3</scene></td></tr>
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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]] 2.18&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1h70|1h70]], [[3bpb|3bpb]]</div></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=HM3:(4-CHLOROPYRIDIN-2-YL)METHANOL'>HM3</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PA1195 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dimethylargininase Dimethylargininase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.18 3.5.3.18] </span></td></tr>
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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=3rhy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rhy OCA], [https://pdbe.org/3rhy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rhy RCSB], [https://www.ebi.ac.uk/pdbsum/3rhy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rhy ProSAT]</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=3rhy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rhy OCA], [https://pdbe.org/3rhy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rhy RCSB], [https://www.ebi.ac.uk/pdbsum/3rhy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rhy ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/DDAH_PSEAE DDAH_PSEAE]] Hydrolyzes N(G),N(G)-dimethyl-L-arginine (ADMA) and N(G)-monomethyl-L-arginine (MMA) which act as inhibitors of NOS.
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[https://www.uniprot.org/uniprot/DDAH_PSEAE DDAH_PSEAE] Hydrolyzes N(G),N(G)-dimethyl-L-arginine (ADMA) and N(G)-monomethyl-L-arginine (MMA) which act as inhibitors of NOS.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Small molecules capable of selective covalent protein modification are of significant interest for the development of biological probes and therapeutics. We recently reported that 2-methyl-4-bromopyridine is a quiescent affinity label for the nitric oxide controlling enzyme dimethylarginine dimethylaminohydrolase (DDAH), raising the possibility that the 4-halopyridine motif may have utility as a moderately-reactive group suitable for wider application. [Johnson, C.M., Linsky, T.W., Yoon, D.W., Person, M.D. &amp; Fast, W. (2011) J. Am. Chem. Soc. 133, 1553-1562] Therefore, the inactivation mechanism of the related compound 2-hydroxymethyl-4-chloropyridine is probed here in more detail. Solution studies support an inactivation mechanism in which the active-site Asp66 residue stabilizes the pyridinium form of the inactivator, which has enhanced reactivity toward the active site Cys, resulting in covalent bond formation, loss of the halide, and irreversible inactivation. A 2.18 A resolution X-ray crystal structure of the inactivated complex elucidates the inactivator's pose and covalent attachment to the active-site Cys, but the conformation does not show an interaction with Asp66. Molecular modeling is used to investigate inactivator binding, reaction, and also a final pyridinium deprotonation step that accounts for the apparent differences between the solution-based and structural studies with respect to the role of Asp66. This work integrates multiple approaches to elucidate the inactivation mechanism of a novel 4-halopyridine "warhead," emphasizing the strategy of using pyridinium formation as a "switch" to enhance reactivity when bound to the target protein.
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On the Mechanism of Dimethylarginine Dimethylaminohydrolase Inactivation by 4-Halopyridines.,Johnson CM, Monzingo AF, Ke Z, Yoon DW, Linsky TW, Guo H, Robertus JD, Fast W J Am Chem Soc. 2011 Jun 1. PMID:21630706<ref>PMID:21630706</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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<div class="pdbe-citations 3rhy" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Dimethylargininase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Fast, W]]
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[[Category: Pseudomonas aeruginosa]]
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[[Category: Guo, H]]
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[[Category: Fast W]]
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[[Category: Johnson, C M]]
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[[Category: Guo H]]
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[[Category: Ke, Z]]
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[[Category: Johnson CM]]
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[[Category: Linsky, T W]]
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[[Category: Ke Z]]
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[[Category: Monzingo, A F]]
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[[Category: Linsky TW]]
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[[Category: Robertus, J D]]
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[[Category: Monzingo AF]]
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[[Category: Yoon, D W]]
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[[Category: Robertus JD]]
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[[Category: Enzyme adduct]]
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[[Category: Yoon D-W]]
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[[Category: Hydrolase]]
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Revision as of 12:24, 14 March 2024

Crystal structure of the dimethylarginine dimethylaminohydrolase adduct with 4-chloro-2-hydroxymethylpyridine

PDB ID 3rhy

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