3nu7: Difference between revisions

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 ==WbpE, an Aminotransferase from Pseudomonas aeruginosa Involved in O-antigen Assembly in Complex with the Cofactor PMP==
-<StructureSection load='3nu7' size='340' side='right' caption='[[3nu7]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='3nu7' size='340' side='right'caption='[[3nu7]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3nu7]] is a 2 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=3NU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NU7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3nu7]] 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=3NU7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NU7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</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]] 1.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3nu8|3nu8]], [[3nub|3nub]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PA3155, wbpE ([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=3nu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nu7 OCA], [https://pdbe.org/3nu7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nu7 RCSB], [https://www.ebi.ac.uk/pdbsum/3nu7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nu7 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=3nu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nu7 OCA], [http://pdbe.org/3nu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nu7 RCSB], [http://www.ebi.ac.uk/pdbsum/3nu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nu7 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/WBPE_PSEAE WBPE_PSEAE]] Plays a role in the biosynthesis of B-band O antigen for serotype O5. Catalyzes the amination of UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronic acid (UDP-3-oxo-D-GlcNAcA) to UDP-2-acetamido-3-amino-2,3-dideoxy-D-glucuronic acid (UDP-GlcNAc3NA), using L-glutamate as the preferred amine donor.<ref>PMID:18621892</ref> <ref>PMID:19282284</ref> <ref>PMID:19348502</ref>
+[https://www.uniprot.org/uniprot/WBPE_PSEAE WBPE_PSEAE] Plays a role in the biosynthesis of B-band O antigen for serotype O5. Catalyzes the amination of UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronic acid (UDP-3-oxo-D-GlcNAcA) to UDP-2-acetamido-3-amino-2,3-dideoxy-D-glucuronic acid (UDP-GlcNAc3NA), using L-glutamate as the preferred amine donor.<ref>PMID:18621892</ref> <ref>PMID:19282284</ref> <ref>PMID:19348502</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/nu/3nu7_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nu/3nu7_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 21: / Line 20: @@
 </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=3nu7 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-In recent years, the opportunistic pathogen Pseudomonas aeruginosa has emerged as a major source of hospital-acquired infections. Effective treatment has proven increasingly difficult due to the spread of multidrug resistant strains and thus requires a deeper understanding of the biochemical mechanisms of pathogenicity. The central carbohydrate of the P. aeruginosa PAO1 (O5) B-band O-antigen, ManNAc(3NAc)A, has been shown to be critical for virulence and is produced in a stepwise manner by five enzymes in the Wbp pathway (WbpA, WbpB, WbpE, WbpD, and WbpI). Herein, we present the crystal structure of the aminotransferase WbpE from P. aeruginosa PAO1 in complex with the cofactor pyridoxal 5'-phosphate (PLP) and product UDP-GlcNAc(3NH(2))A as the external aldimine at 1.9 A resolution. We also report the structures of WbpE in complex with PMP alone as well as the PLP internal aldimine and show that the dimeric structure of WbpE observed in the crystal structure is confirmed by analytical ultracentrifugation. Analysis of these structures reveals that the active site of the enzyme is composed of residues from both subunits. In particular, we show that a key residue (Arg229), which has previously been implicated in direct interactions with the alpha-carboxylate moiety of alpha-ketoglutarate, is also uniquely positioned to bestow specificity for the 6''-carboxyl group of GlcNAc(3NH(2))A through a salt bridge. This finding is intriguing because while an analogous basic residue is present in WbpE homologues that do not process 6''-carboxyl-modified saccharides, recent structural studies reveal that this side chain is retracted to accommodate a neutral C6'' atom. This work represents the first structural analysis of a nucleotide sugar aminotransferase with a bound product modified at the C2'', C3'', and C6'' positions and provides insight into a novel target for treatment of P. aeruginosa infection.
-Structural Analysis of WbpE from Pseudomonas aeruginosa PAO1: A Nucleotide Sugar Aminotransferase Involved in O-Antigen Assembly .,Larkin A, Olivier NB, Imperiali B Biochemistry. 2010 Jul 28. PMID:20604544<ref>PMID:20604544</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3nu7" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Aminotransferase|Aminotransferase]]
+*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Imperiali, B]]
+[[Category: Large Structures]]
-[[Category: Larkin, A]]
+[[Category: Pseudomonas aeruginosa]]
-[[Category: Olivier, N B]]
+[[Category: Imperiali B]]
-[[Category: Aminotransferase]]
+[[Category: Larkin A]]
-[[Category: B-band]]
+[[Category: Olivier NB]]
-[[Category: Domain-swapped beta hairpin]]
-[[Category: Lipopolysaccharide]]
-[[Category: O-antigen]]
-[[Category: Plp]]
-[[Category: Pmp]]
-[[Category: Transferase]]