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| | <StructureSection load='6sm3' size='340' side='right'caption='[[6sm3]], [[Resolution|resolution]] 3.30Å' scene=''> | | <StructureSection load='6sm3' size='340' side='right'caption='[[6sm3]], [[Resolution|resolution]] 3.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6sm3]] is a 3 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=6SM3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SM3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SM3 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=PLM:PALMITIC+ACID'>PLM</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6sli|6sli]], [[6slj|6slj]], [[6sln|6sln]]</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=PLM:PALMITIC+ACID'>PLM</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=6sm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sm3 OCA], [http://pdbe.org/6sm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sm3 RCSB], [http://www.ebi.ac.uk/pdbsum/6sm3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sm3 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=6sm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sm3 OCA], [https://pdbe.org/6sm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sm3 RCSB], [https://www.ebi.ac.uk/pdbsum/6sm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sm3 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: Ranson NA]] |
| - | [[Category: Porphyromonas gingivalis w83]] | + | [[Category: White JBR]] |
| - | [[Category: Berg, B van den]] | + | [[Category: Van den Berg B]] |
| - | [[Category: Ranson, N A]]
| + | |
| - | [[Category: White, J B.R]]
| + | |
| - | [[Category: Beta-barrel]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Omp]]
| + | |
| - | [[Category: Tonb-dependent]]
| + | |
| - | [[Category: 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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