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| | ==Structure of Escherichia coli PgaB 42-655 in complex with nickel== | | ==Structure of Escherichia coli PgaB 42-655 in complex with nickel== |
| - | <StructureSection load='4f9d' size='340' side='right' caption='[[4f9d]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='4f9d' size='340' side='right'caption='[[4f9d]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4f9d]] is a 2 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=4F9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F9D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4f9d]] is a 2 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=4F9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F9D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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">[[4f9j|4f9j]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=4f9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f9d OCA], [https://pdbe.org/4f9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f9d RCSB], [https://www.ebi.ac.uk/pdbsum/4f9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f9d 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=4f9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f9d OCA], [http://pdbe.org/4f9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f9d RCSB], [http://www.ebi.ac.uk/pdbsum/4f9d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f9d 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;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | Exopolysaccharides are required for the development and integrity of biofilms produced by a wide variety of bacteria. In Escherichia coli, partial de-N-acetylation of the exopolysaccharide poly-beta-1,6-N-acetyl-D-glucosamine (PNAG) by the periplasmic protein PgaB is required for polysaccharide intercellular adhesin-dependent biofilm formation. To understand the molecular basis for PNAG de-N-acetylation, the structure of PgaB in complex with Ni(2+) and Fe(3+) have been determined to 1.9 and 2.1 A resolution, respectively, and its activity on beta-1,6-GlcNAc oligomers has been characterized. The structure of PgaB reveals two (beta/alpha)(x) barrel domains: a metal-binding de-N-acetylase that is a member of the family 4 carbohydrate esterases (CE4s) and a domain structurally similar to glycoside hydrolases. PgaB displays de-N-acetylase activity on beta-1,6-GlcNAc oligomers but not on the beta-1,4-(GlcNAc)(4) oligomer chitotetraose and is the first CE4 member to exhibit this substrate specificity. De-N-acetylation occurs in a length-dependent manor, and specificity is observed for the position of de-N-acetylation. A key aspartic acid involved in de-N-acetylation, normally seen in other CE4s, is missing in PgaB, suggesting that the activity of PgaB is attenuated to maintain the low levels of de-N-acetylation of PNAG observed in vivo. The metal dependence of PgaB is different from most CE4s, because PgaB shows increased rates of de-N-acetylation with Co(2+) and Ni(2+) under aerobic conditions, and Co(2+), Ni(2+) and Fe(2+) under anaerobic conditions, but decreased activity with Zn(2+). The work presented herein will guide inhibitor design to combat biofilm formation by E. coli and potentially a wide range of medically relevant bacteria producing polysaccharide intercellular adhesin-dependent biofilms.
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| - | The structure- and metal-dependent activity of Escherichia coli PgaB provides insight into the partial de-N-acetylation of poly-beta-1,6-N-acetyl-D-glucosamine.,Little DJ, Poloczek J, Whitney JC, Robinson H, Nitz M, Howell PL J Biol Chem. 2012 Sep 7;287(37):31126-37. doi: 10.1074/jbc.M112.390005. Epub 2012, Jul 18. PMID:22810235<ref>PMID:22810235</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4f9d" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Howell, P L]] | + | [[Category: Large Structures]] |
| - | [[Category: Little, D J]] | + | [[Category: Howell PL]] |
| - | [[Category: Nitz, M]] | + | [[Category: Little DJ]] |
| - | [[Category: Poloczek, J]] | + | [[Category: Nitz M]] |
| - | [[Category: Robinson, H]] | + | [[Category: Poloczek J]] |
| - | [[Category: Whitney, J C]] | + | [[Category: Robinson H]] |
| - | [[Category: Carbohydrate/sugar binding]]
| + | [[Category: Whitney JC]] |
| - | [[Category: Deacetylase]]
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| - | [[Category: Family 4 carbohydrate esterase]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Tim barrel]]
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