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| | <StructureSection load='6p9d' size='340' side='right'caption='[[6p9d]], [[Resolution|resolution]] 1.33Å' scene=''> | | <StructureSection load='6p9d' size='340' side='right'caption='[[6p9d]], [[Resolution|resolution]] 1.33Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6p9d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P9D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6p9d]] 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=6P9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P9D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.329Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dauA, PA3863 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.99.6 1.4.99.6] </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=6p9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p9d OCA], [https://pdbe.org/6p9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p9d RCSB], [https://www.ebi.ac.uk/pdbsum/6p9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p9d 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=6p9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p9d OCA], [https://pdbe.org/6p9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p9d RCSB], [https://www.ebi.ac.uk/pdbsum/6p9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p9d ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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>
| + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Oxidoreductase]] | + | [[Category: Pseudomonas aeruginosa PAO1]] |
| - | [[Category: Pseae]]
| + | [[Category: Agniswamy J]] |
| - | [[Category: Agniswamy, J]] | + | [[Category: Gadda G]] |
| - | [[Category: Gadda, G]] | + | [[Category: Gannavaram S]] |
| - | [[Category: Gannavaram, S]] | + | [[Category: Iyer A]] |
| - | [[Category: Iyer, A]] | + | [[Category: Reis RAG]] |
| - | [[Category: Reis, R A.G]] | + | [[Category: Weber I]] |
| - | [[Category: Weber, I]] | + | |
| - | [[Category: Dehydrogenase pseudomonas aeruginosa 6-oh-fad d-amino acid]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| Structural highlights
Function
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).[1] [2] [3] [4] [5]
Publication Abstract from PubMed
Proteins are inherently dynamic, and proper enzyme function relies on conformational flexibility. In this study, we demonstrated how an active site residue changes an enzyme's reactivity by modulating fluctuations between conformational states. Replacement of tyrosine 249 (Y249) with phenylalanine in the active site of the flavin-dependent d-arginine dehydrogenase yielded an enzyme with both an active yellow FAD (Y249F-y) and an inactive chemically modified green FAD, identified as 6-OH-FAD (Y249F-g) through various spectroscopic techniques. Structural investigation of Y249F-g and Y249F-y variants by comparison to the wild-type enzyme showed no differences in the overall protein structure and fold. A closer observation of the active site of the Y249F-y enzyme revealed an alternative conformation for some active site residues and the flavin cofactor. Molecular dynamics simulations probed the alternate conformations observed in the Y249F-y enzyme structure and showed that the enzyme variant with FAD samples a metastable conformational state, not available to the wild-type enzyme. Hybrid quantum/molecular mechanical calculations identified differences in flavin electronics between the wild type and the alternate conformation of the Y249F-y enzyme. The computational studies further indicated that the alternate conformation in the Y249F-y enzyme is responsible for the higher spin density at the C6 atom of flavin, which is consistent with the formation of 6-OH-FAD in the variant enzyme. The observations in this study are consistent with an alternate conformational space that results in fine-tuning the microenvironment around a versatile cofactor playing a critical role in enzyme function.
A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity.,Iyer A, Reis RAG, Gannavaram S, Momin M, Spring-Connell AM, Orozco-Gonzalez Y, Agniswamy J, Hamelberg D, Weber IT, Gozem S, Wang S, Germann MW, Gadda G Biochemistry. 2021 Mar 9;60(9):711-724. doi: 10.1021/acs.biochem.1c00054. Epub, 2021 Feb 25. PMID:33630571[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Li C, Lu CD. Arginine racemization by coupled catabolic and anabolic dehydrogenases. Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):906-11. doi:, 10.1073/pnas.0808269106. Epub 2009 Jan 12. PMID:19139398 doi:http://dx.doi.org/10.1073/pnas.0808269106
- ↑ Li C, Yao X, Lu CD. Regulation of the dauBAR operon and characterization of D-amino acid dehydrogenase DauA in arginine and lysine catabolism of Pseudomonas aeruginosa PAO1. Microbiology (Reading). 2010 Jan;156(Pt 1):60-71. doi: 10.1099/mic.0.033282-0., Epub 2009 Oct 22. PMID:19850617 doi:http://dx.doi.org/10.1099/mic.0.033282-0
- ↑ Fu G, Yuan H, Li C, Lu CD, Gadda G, Weber IT. Conformational Changes and Substrate Recognition in Pseudomonas aeruginosa d-Arginine Dehydrogenase (,). Biochemistry. 2010 Sep 9. PMID:20809650 doi:10.1021/bi1005865
- ↑ Oliver KE, Silo-Suh L. Impact of D-amino acid dehydrogenase on virulence factor production by a Pseudomonas aeruginosa. Can J Microbiol. 2013 Sep;59(9):598-603. doi: 10.1139/cjm-2013-0289. Epub 2013, Jul 11. PMID:24011342 doi:http://dx.doi.org/10.1139/cjm-2013-0289
- ↑ Jann A, Matsumoto H, Haas D. The fourth arginine catabolic pathway of Pseudomonas aeruginosa. J Gen Microbiol. 1988 Apr;134(4):1043-53. doi: 10.1099/00221287-134-4-1043. PMID:3141581 doi:http://dx.doi.org/10.1099/00221287-134-4-1043
- ↑ Iyer A, Reis RAG, Gannavaram S, Momin M, Spring-Connell AM, Orozco-Gonzalez Y, Agniswamy J, Hamelberg D, Weber IT, Gozem S, Wang S, Germann MW, Gadda G. A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity. Biochemistry. 2021 Mar 9;60(9):711-724. doi: 10.1021/acs.biochem.1c00054. Epub, 2021 Feb 25. PMID:33630571 doi:http://dx.doi.org/10.1021/acs.biochem.1c00054
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