|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==WbpE, an Aminotransferase from Pseudomonas aeruginosa Involved in O-antigen Assembly in Complex with Product as the External Aldimine== | | ==WbpE, an Aminotransferase from Pseudomonas aeruginosa Involved in O-antigen Assembly in Complex with Product as the External Aldimine== |
| - | <StructureSection load='3nub' size='340' side='right' caption='[[3nub]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='3nub' size='340' side='right'caption='[[3nub]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3nub]] 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=3NUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NUB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3nub]] 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=3NUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NUB 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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UD0:(2S,3S,4R,5R,6R)-5-(ACETYLAMINO)-6-{[(S)-{[(S)-{[(2S,3R,4S,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-3-HYDROXY-4-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}TETRAHYDRO-2H-PYRAN-2-CARBOXYLIC+ACID'>UD0</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3nu7|3nu7]], [[3nu8|3nu8]]</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UD0:(2S,3S,4R,5R,6R)-5-(ACETYLAMINO)-6-{[(S)-{[(S)-{[(2S,3R,4S,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-3-HYDROXY-4-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}TETRAHYDRO-2H-PYRAN-2-CARBOXYLIC+ACID'>UD0</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=3nub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nub OCA], [https://pdbe.org/3nub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nub RCSB], [https://www.ebi.ac.uk/pdbsum/3nub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nub 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=3nub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nub OCA], [http://pdbe.org/3nub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nub RCSB], [http://www.ebi.ac.uk/pdbsum/3nub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nub ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nu/3nub_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nu/3nub_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| Line 32: |
Line 31: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Aminotransferase|Aminotransferase]] | + | *[[Aminotransferase 3D structures|Aminotransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Imperiali, B]] | + | [[Category: Large Structures]] |
| - | [[Category: Larkin, A]]
| + | |
| - | [[Category: Olivier, N B]]
| + | |
| - | [[Category: Aminotransferase]]
| + | |
| - | [[Category: B-band]]
| + | |
| - | [[Category: Domain-swapped beta hairpin]]
| + | |
| - | [[Category: External aldimine]]
| + | |
| - | [[Category: Lipopolysaccharide]]
| + | |
| - | [[Category: O-antigen]]
| + | |
| - | [[Category: Plp]]
| + | |
| - | [[Category: Pmp]]
| + | |
| | [[Category: Pseudomonas aeruginosa]] | | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Transferase]] | + | [[Category: Imperiali B]] |
| | + | [[Category: Larkin A]] |
| | + | [[Category: Olivier NB]] |
| Structural highlights
Function
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.[1] [2] [3]
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
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[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Westman EL, Preston A, Field RA, Lam JS. Biosynthesis of a rare di-N-acetylated sugar in the lipopolysaccharides of both Pseudomonas aeruginosa and Bordetella pertussis occurs via an identical scheme despite different gene clusters. J Bacteriol. 2008 Sep;190(18):6060-9. doi: 10.1128/JB.00579-08. Epub 2008 Jul 11. PMID:18621892 doi:10.1128/JB.00579-08
- ↑ Westman EL, McNally DJ, Charchoglyan A, Brewer D, Field RA, Lam JS. Characterization of WbpB, WbpE, and WbpD and reconstitution of a pathway for the biosynthesis of UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronic acid in Pseudomonas aeruginosa. J Biol Chem. 2009 May 1;284(18):11854-62. doi: 10.1074/jbc.M808583200. Epub 2009 , Mar 12. PMID:19282284 doi:10.1074/jbc.M808583200
- ↑ Larkin A, Imperiali B. Biosynthesis of UDP-GlcNAc(3NAc)A by WbpB, WbpE, and WbpD: enzymes in the Wbp pathway responsible for O-antigen assembly in Pseudomonas aeruginosa PAO1. Biochemistry. 2009 Jun 16;48(23):5446-55. doi: 10.1021/bi900186u. PMID:19348502 doi:10.1021/bi900186u
- ↑ Larkin A, Olivier NB, Imperiali B. Structural Analysis of WbpE from Pseudomonas aeruginosa PAO1: A Nucleotide Sugar Aminotransferase Involved in O-Antigen Assembly . Biochemistry. 2010 Jul 28. PMID:20604544 doi:10.1021/bi100805b
|
