7rdf
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F co-crystallized in the presence of D-arginine== | ==Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F co-crystallized in the presence of D-arginine== | ||
| - | <StructureSection load='7rdf' size='340' side='right'caption='[[7rdf]]' scene=''> | + | <StructureSection load='7rdf' size='340' side='right'caption='[[7rdf]], [[Resolution|resolution]] 1.29Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RDF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7rdf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RDF FirstGlance]. <br> |
| - | </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=7rdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rdf OCA], [https://pdbe.org/7rdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rdf RCSB], [https://www.ebi.ac.uk/pdbsum/7rdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rdf ProSAT]</span></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]] 1.29Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4R2:[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{S})-5-[5-[(~{E})-4-carbamimidamidobut-2-enoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl]+hydrogen+phosphate'>4R2</scene>, <scene name='pdbligand=6FA:6-HYDROXY-FLAVIN-ADENINE+DINUCLEOTIDE'>6FA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=7rdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rdf OCA], [https://pdbe.org/7rdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rdf RCSB], [https://www.ebi.ac.uk/pdbsum/7rdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rdf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/DAUA_PSEAE DAUA_PSEAE] DauA is highly expressed within the cystic fibrosis (CF) lung, and it is required for virulence via the optimal production of hydrogen cyanide, pyocyanine, pyoverdine, rhamnolipid and alginate during biofilm formation (PubMed:24011342). Involved in the catabolism of D-lysine and D-arginine. Under aerobic conditions, the arginine succinyltransferase (AST) and arginine transaminase (ATA) pathways are 2 major routes for L-arginine utilization as the sole source of carbon and nitrogen. The D-to-L racemization of arginine by DauA and DauB is necessary, before to be channeled into the AST and/or ATA pathways. DauA catalyzes the flavin-dependent oxidative deamination of D-arginine into 2-ketoarginine (2-KA) and ammonia (PubMed:3141581, PubMed:19139398, PubMed:19850617, PubMed:20809650). It has also dehydrogenase activity towards D-lysine, D-tyrosine, D-methionine, D-phenylalanine, D-ornithine, D-histidine and D-leucine as substrates (PubMed:19850617, PubMed:20809650).<ref>PMID:19139398</ref> <ref>PMID:19850617</ref> <ref>PMID:20809650</ref> <ref>PMID:24011342</ref> <ref>PMID:3141581</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) catalyzes the flavin-dependent oxidation of d-arginine and other d-amino acids. Here, we report the crystal structure at 1.29 A resolution for PaDADH-Y249F expressed and co-crystallized with d-arginine. The overall structure of PaDADH-Y249F resembled PaDADH-WT, but the electron density for the flavin cofactor was ambiguous, suggesting the presence of modified flavins. Electron density maps and mass spectrometric analysis confirmed the presence of both N5-(4-guanidino-oxobutyl)-FAD and 6-OH-FAD in a single crystal of PaDADH-Y249F and helped with the further refinement of the X-ray crystal structure. The versatility of the reduced flavin is apparent in the PaDADH-Y249F structure and is evidenced by the multiple functions it can perform in the same active site. | ||
| + | |||
| + | Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase.,Iyer A, Reis RAG, Agniswamy J, Weber IT, Gadda G Arch Biochem Biophys. 2022 Jan 15;715:109100. doi: 10.1016/j.abb.2021.109100., Epub 2021 Dec 2. PMID:34864048<ref>PMID:34864048</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7rdf" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Pseudomonas aeruginosa PAO1]] | ||
[[Category: Agniswamy A]] | [[Category: Agniswamy A]] | ||
[[Category: Gadda G]] | [[Category: Gadda G]] | ||
Current revision
Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F co-crystallized in the presence of D-arginine
| |||||||||||
