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3nyf

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Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with Imino-Histidine

Structural highlights

3nyf is a 1 chain structure with sequence from Pseudomonas aeruginosa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

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

DADH catalyzes the flavin-dependent oxidative deamination of d-amino acids to the corresponding alpha-keto acids and ammonia. Here we report the first X-ray crystal structures of DADH at 1.06 A resolution and its complexes with iminoarginine (DADH(red)/iminoarginine) and iminohistidine (DADH(red)/iminohistidine) at 1.30 A resolution. The DADH crystal structure comprises an unliganded conformation and a product-bound conformation, which is almost identical to the DADH(red)/iminoarginine crystal structure. The active site of DADH was partially occupied with iminoarginine product (30% occupancy) that interacts with Tyr53 in the minor conformation of a surface loop. This flexible loop forms an "active site lid", similar to those seen in other enzymes, and may play an essential role in substrate recognition. The guanidinium side chain of iminoarginine forms a hydrogen bond interaction with the hydroxyl of Thr50 and an ionic interaction with Glu87. In the structure of DADH in complex with iminohistidine, two alternate conformations were observed for iminohistidine where the imidazole groups formed hydrogen bond interactions with the side chains of His48 and Thr50 and either Glu87 or Gln336. The different interactions and very distinct binding modes observed for iminoarginine and iminohistidine are consistent with the 1000-fold difference in k(cat)/K(m) values for d-arginine and d-histidine. Comparison of the kinetic data for the activity of DADH on different d-amino acids and the crystal structures in complex with iminoarginine and iminohistidine establishes that this enzyme is characterized by relatively broad substrate specificity, being able to oxidize positively charged and large hydrophobic d-amino acids bound within a flask-like cavity.

Conformational Changes and Substrate Recognition in Pseudomonas aeruginosa d-Arginine Dehydrogenase (,).,Fu G, Yuan H, Li C, Lu CD, Gadda G, Weber IT Biochemistry. 2010 Sep 9. PMID:20809650^[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
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3nyf"

Categories: Large Structures | Pseudomonas aeruginosa | Fu G | Weber IT

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with Imino-Histidine==
-<StructureSection load='3nyf' size='340' side='right' caption='[[3nyf]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+<StructureSection load='3nyf' size='340' side='right'caption='[[3nyf]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3nyf]] is a 1 chain structure with sequence 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=3NYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NYF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3nyf]] is a 1 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=3NYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HHI:(2Z)-3-(1H-IMIDAZOL-5-YL)-2-IMINOPROPANOIC+ACID'>HHI</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]] 1.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3nyc|3nyc]], [[3nye|3nye]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HHI:(2Z)-3-(1H-IMIDAZOL-5-YL)-2-IMINOPROPANOIC+ACID'>HHI</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PA3863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</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=3nyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyf OCA], [https://pdbe.org/3nyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nyf RCSB], [https://www.ebi.ac.uk/pdbsum/3nyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyf ProSAT]</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=3nyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nyf RCSB], [http://www.ebi.ac.uk/pdbsum/3nyf PDBsum]</span></td></tr>
 </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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/3nyf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/3nyf_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3nyf ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3nyf" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Pseudomonas aeruginosa]]
-[[Category: Fu, G]]
+[[Category: Fu G]]
-[[Category: Weber, I T]]
+[[Category: Weber IT]]
-[[Category: D-arginine dehydrogenase]]
-[[Category: Fad]]
-[[Category: Imino-histidine]]
-[[Category: Oxidoreductase]]

3nyf

From Proteopedia

Current revision

Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with Imino-Histidine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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