6jzk

From Proteopedia

(Difference between revisions)

Current revision

Structure of FimA type-1 (FimA1) prepilin of the type V major fimbrium

Structural highlights

6jzk is a 2 chain structure with sequence from Porphyromonas gingivalis ATCC 33277. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FIMA1_PORG3 Structural subunit of the major fimbriae. These long, filamentous pili are attached to the cell surface; they mediate biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome (PubMed:9786913, PubMed:12593606, PubMed:15165251, PubMed:17675496, PubMed:17526848, PubMed:20530728, PubMed:27062925). They play an important role in the invasion of periodontal tissues (PubMed:12593606). Fimbriae and their constituents are major virulence factors. FimA proteins from different strains have highly divergent sequences, and this has been used for classification (PubMed:23809984). The sequence-based classification correlates with pathogenicity (PubMed:17675496).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

Publication Abstract from PubMed

Bacterial adhesion is a general strategy for host-microbe and microbe-microbe interactions. Adhesive pili are essential for colonization, biofilm formation, virulence and pathogenesis of many environmental and pathogenic bacteria(1,2). Members of the class Bacteroidia have unique type V pili, assembled by protease-mediated polymerization(3). Porphyromonas gingivalis is the main contributor to periodontal disease and its type V pili are a key factor for its virulence(4). However, the structure of the polymerized pilus and its assembly mechanism are unknown. Here we show structures of polymerized and monomeric states of FimA stalk pilin from P. gingivalis, determined by cryo-electron microscopy and crystallography. The atomic model of assembled FimA shows that the C-terminal strand of a donor subunit is inserted into a groove in the beta-sheet of an acceptor subunit after N-terminal cleavage by the protease RgpB. The C terminus of the donor strand is essential for polymerization. We propose that type V pili assemble via a sequential polar assembly mechanism at the cell surface, involving protease-mediated strand exchange, employed by various Gram-negative species belonging to the class Bacteroidia. Our results reveal functional surfaces related to pathogenic properties of polymerized FimA. These insights may facilitate development of antibacterial drugs.

Structure of polymerized type V pilin reveals assembly mechanism involving protease-mediated strand exchange.,Shibata S, Shoji M, Okada K, Matsunami H, Matthews MM, Imada K, Nakayama K, Wolf M Nat Microbiol. 2020 Apr 13. pii: 10.1038/s41564-020-0705-1. doi:, 10.1038/s41564-020-0705-1. PMID:32284566^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Umemoto T, Hamada N. Characterization of biologically active cell surface components of a periodontal pathogen. The roles of major and minor fimbriae of Porphyromonas gingivalis. J Periodontol. 2003 Jan;74(1):119-22. doi: 10.1902/jop.2003.74.1.119. PMID:12593606 doi:http://dx.doi.org/10.1902/jop.2003.74.1.119
↑ Shoji M, Naito M, Yukitake H, Sato K, Sakai E, Ohara N, Nakayama K. The major structural components of two cell surface filaments of Porphyromonas gingivalis are matured through lipoprotein precursors. Mol Microbiol. 2004 Jun;52(5):1513-25. doi: 10.1111/j.1365-2958.2004.04105.x. PMID:15165251 doi:http://dx.doi.org/10.1111/j.1365-2958.2004.04105.x
↑ Nishiyama SI, Murakami Y, Nagata H, Shizukuishi S, Kawagishi I, Yoshimura F. Involvement of minor components associated with the FimA fimbriae of Porphyromonas gingivalis in adhesive functions. Microbiology. 2007 Jun;153(Pt 6):1916-1925. doi: 10.1099/mic.0.2006/005561-0. PMID:17526848 doi:http://dx.doi.org/10.1099/mic.0.2006/005561-0
↑ Wang M, Shakhatreh MA, James D, Liang S, Nishiyama S, Yoshimura F, Demuth DR, Hajishengallis G. Fimbrial proteins of porphyromonas gingivalis mediate in vivo virulence and exploit TLR2 and complement receptor 3 to persist in macrophages. J Immunol. 2007 Aug 15;179(4):2349-58. doi: 10.4049/jimmunol.179.4.2349. PMID:17675496 doi:http://dx.doi.org/10.4049/jimmunol.179.4.2349
↑ Nagano K, Hasegawa Y, Murakami Y, Nishiyama S, Yoshimura F. FimB regulates FimA fimbriation in Porphyromonas gingivalis. J Dent Res. 2010 Sep;89(9):903-8. doi: 10.1177/0022034510370089. Epub 2010 Jun 8. PMID:20530728 doi:http://dx.doi.org/10.1177/0022034510370089
↑ Nagano K, Abiko Y, Yoshida Y, Yoshimura F. Genetic and antigenic analyses of Porphyromonas gingivalis FimA fimbriae. Mol Oral Microbiol. 2013 Oct;28(5):392-403. doi: 10.1111/omi.12032. Epub 2013 Jul, 1. PMID:23809984 doi:http://dx.doi.org/10.1111/omi.12032
↑ Xu Q, Shoji M, Shibata S, Naito M, Sato K, Elsliger MA, Grant JC, Axelrod HL, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Deacon AM, Godzik A, Lesley SA, Curtis MA, Nakayama K, Wilson IA. A Distinct Type of Pilus from the Human Microbiome. Cell. 2016 Apr 21;165(3):690-703. doi: 10.1016/j.cell.2016.03.016. Epub 2016 Apr , 7. PMID:27062925 doi:http://dx.doi.org/10.1016/j.cell.2016.03.016
↑ Kadowaki T, Nakayama K, Yoshimura F, Okamoto K, Abe N, Yamamoto K. Arg-gingipain acts as a major processing enzyme for various cell surface proteins in Porphyromonas gingivalis. J Biol Chem. 1998 Oct 30;273(44):29072-6. doi: 10.1074/jbc.273.44.29072. PMID:9786913 doi:http://dx.doi.org/10.1074/jbc.273.44.29072
↑ Shibata S, Shoji M, Okada K, Matsunami H, Matthews MM, Imada K, Nakayama K, Wolf M. Structure of polymerized type V pilin reveals assembly mechanism involving protease-mediated strand exchange. Nat Microbiol. 2020 Apr 13. pii: 10.1038/s41564-020-0705-1. doi:, 10.1038/s41564-020-0705-1. PMID:32284566 doi:http://dx.doi.org/10.1038/s41564-020-0705-1

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6jzk"

@@ Line 3: / Line 3: @@
 <StructureSection load='6jzk' size='340' side='right'caption='[[6jzk]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6jzk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Porg3 Porg3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JZK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JZK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6jzk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis_ATCC_33277 Porphyromonas gingivalis ATCC 33277]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JZK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JZK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SRT:S,R+MESO-TARTARIC+ACID'>SRT</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6jzj|6jzj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SRT:S,R+MESO-TARTARIC+ACID'>SRT</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fimA, PGN_0180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=431947 PORG3])</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=6jzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jzk OCA], [https://pdbe.org/6jzk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jzk RCSB], [https://www.ebi.ac.uk/pdbsum/6jzk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jzk ProSAT]</span></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=6jzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jzk OCA], [http://pdbe.org/6jzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jzk RCSB], [http://www.ebi.ac.uk/pdbsum/6jzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jzk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/FIMA1_PORG3 FIMA1_PORG3]] Structural subunit of the major fimbriae. These long, filamentous pili are attached to the cell surface; they mediate biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome (PubMed:9786913, PubMed:12593606, PubMed:15165251, PubMed:17675496, PubMed:17526848, PubMed:20530728, PubMed:27062925). They play an important role in the invasion of periodontal tissues (PubMed:12593606). Fimbriae and their constituents are major virulence factors. FimA proteins from different strains have highly divergent sequences, and this has been used for classification (PubMed:23809984). The sequence-based classification correlates with pathogenicity (PubMed:17675496).<ref>PMID:12593606</ref> <ref>PMID:15165251</ref> <ref>PMID:17526848</ref> <ref>PMID:17675496</ref> <ref>PMID:20530728</ref> <ref>PMID:23809984</ref> <ref>PMID:27062925</ref> <ref>PMID:9786913</ref>
+[https://www.uniprot.org/uniprot/FIMA1_PORG3 FIMA1_PORG3] Structural subunit of the major fimbriae. These long, filamentous pili are attached to the cell surface; they mediate biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome (PubMed:9786913, PubMed:12593606, PubMed:15165251, PubMed:17675496, PubMed:17526848, PubMed:20530728, PubMed:27062925). They play an important role in the invasion of periodontal tissues (PubMed:12593606). Fimbriae and their constituents are major virulence factors. FimA proteins from different strains have highly divergent sequences, and this has been used for classification (PubMed:23809984). The sequence-based classification correlates with pathogenicity (PubMed:17675496).<ref>PMID:12593606</ref> <ref>PMID:15165251</ref> <ref>PMID:17526848</ref> <ref>PMID:17675496</ref> <ref>PMID:20530728</ref> <ref>PMID:23809984</ref> <ref>PMID:27062925</ref> <ref>PMID:9786913</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Porg3]]
+[[Category: Porphyromonas gingivalis ATCC 33277]]
-[[Category: Imada, K]]
+[[Category: Imada K]]
-[[Category: Nakayam, K]]
+[[Category: Nakayam K]]
-[[Category: Okada, K]]
+[[Category: Okada K]]
-[[Category: Shoji, M]]
+[[Category: Shoji M]]
-[[Category: Cell adhesion]]
-[[Category: Major fimbrial subunit protein]]
-[[Category: Type v pili]]

6jzk

From Proteopedia

Current revision

Structure of FimA type-1 (FimA1) prepilin of the type V major fimbrium

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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