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| | <StructureSection load='4p7r' size='340' side='right'caption='[[4p7r]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='4p7r' size='340' side='right'caption='[[4p7r]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4p7r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P7R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4p7r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P7R FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4p7l|4p7l]], [[4p7n|4p7n]], [[4p7o|4p7o]], [[4p7q|4p7q]]</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=4p7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p7r OCA], [https://pdbe.org/4p7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p7r RCSB], [https://www.ebi.ac.uk/pdbsum/4p7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p7r ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pgaB, ycdR, b1023, JW5142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4p7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p7r OCA], [http://pdbe.org/4p7r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4p7r RCSB], [http://www.ebi.ac.uk/pdbsum/4p7r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4p7r ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PGAB_ECOLI PGAB_ECOLI]] Catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PGA), a biofilm adhesin polysaccharide. N-deacetylation promotes PGA export through the PgaA porin.<ref>PMID:15090514</ref> <ref>PMID:18359807</ref> | + | [https://www.uniprot.org/uniprot/PGAB_ECOLI PGAB_ECOLI] Catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PGA), a biofilm adhesin polysaccharide. N-deacetylation promotes PGA export through the PgaA porin.<ref>PMID:15090514</ref> <ref>PMID:18359807</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bamford, N C]] | + | [[Category: Bamford NC]] |
| - | [[Category: DiFrancesco, B]] | + | [[Category: DiFrancesco B]] |
| - | [[Category: Howell, P L]] | + | [[Category: Howell PL]] |
| - | [[Category: Ing, C]] | + | [[Category: Ing C]] |
| - | [[Category: Li, G]] | + | [[Category: Li G]] |
| - | [[Category: Little, D J]] | + | [[Category: Little DJ]] |
| - | [[Category: Nitz, M]] | + | [[Category: Nitz M]] |
| - | [[Category: Pomes, R]] | + | [[Category: Pomes R]] |
| - | [[Category: Robinson, H]] | + | [[Category: Robinson H]] |
| - | [[Category: Beta alpha barrel]]
| + | |
| - | [[Category: Carbohydrate binding]]
| + | |
| - | [[Category: Complex]]
| + | |
| - | [[Category: Glycosyl hydrolase fold]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
PGAB_ECOLI Catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PGA), a biofilm adhesin polysaccharide. N-deacetylation promotes PGA export through the PgaA porin.[1] [2]
Publication Abstract from PubMed
Poly-beta-1,6-N-acetyl-d-glucosamine (PNAG) is an exopolysaccharide produced by a wide variety of medically important bacteria. Polyglucosamine subunit B (PgaB) is responsible for the de-N-acetylation of PNAG, a process required for polymer export and biofilm formation. PgaB is located in the periplasm and likely bridges the inner membrane synthesis and outer membrane export machinery. Here, we present structural, functional, and molecular simulation data that suggest PgaB associates with PNAG continuously during periplasmic transport. We show that the association of PgaB's N- and C-terminal domains forms a cleft required for the binding and de-N-acetylation of PNAG. Molecular dynamics (MD) simulations of PgaB show a binding preference for N-acetylglucosamine (GlcNAc) to the N-terminal domain and glucosammonium to the C-terminal domain. Continuous ligand binding density is observed that extends around PgaB from the N-terminal domain active site to an electronegative groove on the C-terminal domain that would allow for a processive mechanism. PgaB's C-terminal domain (PgaB310-672) directly binds PNAG oligomers with dissociation constants of approximately 1-3 mM, and the structures of PgaB310-672 in complex with beta-1,6-(GlcNAc)6, GlcNAc, and glucosamine reveal a unique binding mode suitable for interaction with de-N-acetylated PNAG (dPNAG). Furthermore, PgaB310-672 contains a beta-hairpin loop (betaHL) important for binding PNAG that was disordered in previous PgaB42-655 structures and is highly dynamic in the MD simulations. We propose that conformational changes in PgaB310-672 mediated by the betaHL on binding of PNAG/dPNAG play an important role in the targeting of the polymer for export and its release.
Modification and periplasmic translocation of the biofilm exopolysaccharide poly-beta-1,6-N-acetyl-d-glucosamine.,Little DJ, Li G, Ing C, DiFrancesco BR, Bamford NC, Robinson H, Nitz M, Pomes R, Howell PL Proc Natl Acad Sci U S A. 2014 Jul 3. pii: 201406388. PMID:24994902[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wang X, Preston JF 3rd, Romeo T. The pgaABCD locus of Escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation. J Bacteriol. 2004 May;186(9):2724-34. PMID:15090514
- ↑ Itoh Y, Rice JD, Goller C, Pannuri A, Taylor J, Meisner J, Beveridge TJ, Preston JF 3rd, Romeo T. Roles of pgaABCD genes in synthesis, modification, and export of the Escherichia coli biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine. J Bacteriol. 2008 May;190(10):3670-80. doi: 10.1128/JB.01920-07. Epub 2008 Mar, 21. PMID:18359807 doi:10.1128/JB.01920-07
- ↑ Little DJ, Li G, Ing C, DiFrancesco BR, Bamford NC, Robinson H, Nitz M, Pomes R, Howell PL. Modification and periplasmic translocation of the biofilm exopolysaccharide poly-beta-1,6-N-acetyl-d-glucosamine. Proc Natl Acad Sci U S A. 2014 Jul 3. pii: 201406388. PMID:24994902 doi:http://dx.doi.org/10.1073/pnas.1406388111
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