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| | <StructureSection load='6sli' size='340' side='right'caption='[[6sli]], [[Resolution|resolution]] 3.38Å' scene=''> | | <StructureSection load='6sli' size='340' side='right'caption='[[6sli]], [[Resolution|resolution]] 3.38Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6sli]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Porgi Porgi] and [http://en.wikipedia.org/wiki/Porphyromonas_gingivalis_w83 Porphyromonas gingivalis w83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SLI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SLI FirstGlance]. <br> | + | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SLI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5PL:(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL+15-METHYLHEXADECANOATE'>5PL</scene>, <scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</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]] 3.38Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ragB, PG_0186 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=242619 PORGI])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5PL:(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL+15-METHYLHEXADECANOATE'>5PL</scene>, <scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6sli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sli OCA], [http://pdbe.org/6sli PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sli RCSB], [http://www.ebi.ac.uk/pdbsum/6sli PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sli ProSAT]</span></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=6sli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sli OCA], [https://pdbe.org/6sli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sli RCSB], [https://www.ebi.ac.uk/pdbsum/6sli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sli ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Porgi]]
| + | [[Category: Madej M]] |
| - | [[Category: Porphyromonas gingivalis w83]]
| + | [[Category: Ranson NA]] |
| - | [[Category: Madej, M]] | + | [[Category: White JBR]] |
| - | [[Category: Ranson, N A]] | + | |
| - | [[Category: White, J B.R]] | + | |
| - | [[Category: Bacteroidete]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Outer membrane protein]]
| + | |
| - | [[Category: Tonb dependent transporter]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how these peptides enter the cell is not clear. Here, we identify RagAB as the outer-membrane importer for these peptides. X-ray crystal structures show that the transporter forms a dimeric RagA2B2 complex, with the RagB substrate-binding surface-anchored lipoprotein forming a closed lid on the RagA TonB-dependent transporter. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a 'pedal bin' mechanism of nutrient uptake. Together with mutagenesis, peptide-binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic, selective outer-membrane oligopeptide-acquisition machine that is essential for the efficient utilization of proteinaceous nutrients by P. gingivalis.
Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis.,Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Basle A, Ranson NA, Potempa J, van den Berg B Nat Microbiol. 2020 May 11. pii: 10.1038/s41564-020-0716-y. doi:, 10.1038/s41564-020-0716-y. PMID:32393857[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Basle A, Ranson NA, Potempa J, van den Berg B. Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis. Nat Microbiol. 2020 May 11. pii: 10.1038/s41564-020-0716-y. doi:, 10.1038/s41564-020-0716-y. PMID:32393857 doi:http://dx.doi.org/10.1038/s41564-020-0716-y
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