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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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4f9j|4f9j]]</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='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=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;"> | | <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: 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]]
| + | |
| - | [[Category: Family 4 carbohydrate esterase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| 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
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.
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[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, Poloczek J, Whitney JC, Robinson H, Nitz M, Howell PL. 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. J Biol Chem. 2012 Sep 7;287(37):31126-37. doi: 10.1074/jbc.M112.390005. Epub 2012, Jul 18. PMID:22810235 doi:10.1074/jbc.M112.390005
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