Summary: Outer membrane usher protein
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This is the Wikipedia entry entitled "Fimbrial usher protein". More...
Fimbrial usher protein Edit Wikipedia article
Fimbrial Usher protein | |||||||||
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![]() Structure of the type 1 pilus assembly platform FimD(25-139).[1] | |||||||||
Identifiers | |||||||||
Symbol | Usher | ||||||||
Pfam | PF00577 | ||||||||
InterPro | IPR000015 | ||||||||
PROSITE | PDOC00886 | ||||||||
TCDB | 1.B.11 | ||||||||
OPM superfamily | 187 | ||||||||
OPM protein | 4j3o | ||||||||
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The fimbrial usher protein is involved in biogenesis of the pilus in Gram-negative bacteria. The biogenesis of fimbriae (or pili) requires a two-component assembly and transport system which is composed of a periplasmic chaperone and an outer membrane protein which has been termed a molecular 'usher'.[2][3][4]
The usher protein has a molecular weight ranging from 86 to 100 kDa and is composed of a membrane-spanning 24-stranded beta barrel domain, reminiscent of porins, and of four periplasmic soluble domains: an N-terminal one of about 120 residues (NTD),[1] a 'middle' domain of about 80 residues[5] located as a soluble insertion within the beta barrel region of the sequence (plug domain) and two IG-like domains (each about 80 residues long) at the C-terminus (CTD1 and CTD2).[6] Although the degree of sequence similarity of these proteins is not very high they share a number of characteristics. One of these is the presence of two pairs of disulfide bond-forming cysteines, the first one located in the NTD and the second in CTD2. The best conserved region of the sequence corresponds to the plug domain.
References
- ^ a b Nishiyama M, Horst R, Eidam O, et al. (June 2005). "Structural basis of chaperone–subunit complex recognition by the type 1 pilus assembly platform FimD". EMBO J. 24 (12): 2075–86. doi:10.1038/sj.emboj.7600693. PMC 1150887. PMID 15920478.
- ^ Hultgren SJ, Jacob-Dubuisson F, Striker R (1994). "Chaperone-assisted self-assembly of pili independent of cellular energy". J. Biol. Chem. 269 (17): 12447–12455. PMID 7909802.
- ^ Schifferli DM, Alrutz MA (1994). "Permissive linker insertion sites in the outer membrane protein of 987P fimbriae of Escherichia coli". J. Bacteriol. 176 (4): 1099–1110. PMC 205162. PMID 7906265.
- ^ Saier Jr MH, Van Rosmalen M (1993). "Structural and evolutionary relationships between two families of bacterial extracytoplasmic chaperone proteins which function cooperatively in fimbrial assembly". Res. Microbiol. 144 (7): 507–527. doi:10.1016/0923-2508(93)90001-I. PMID 7906046.
- ^ Capitani G, Eidam O, Grütter MG (2006). "Evidence for a novel domain of bacterial outer membrane ushers". Proteins. 65 (4): 816–23. doi:10.1002/prot.21147. PMID 17066380.
- ^ Phan G, Remaut H, Wang T, Allen WJ, Pirker KF, Lebedev A, et al. (2011). "Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate". Nature. 474 (7349): 49–53. doi:10.1038/nature10109. PMC 3162478. PMID 21637253.
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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Outer membrane usher protein Provide feedback
In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two- component assembly and transport system which is composed of a periplasmic chaperone and an outer membrane protein which has been termed a molecular 'usher' [1-3]. The usher protein is rather large (from 86 to 100 Kd) and seems to be mainly composed of membrane-spanning beta-sheets, a structure reminiscent of porins. Although the degree of sequence similarity of these proteins is not very high they share a number of characteristics. One of these is the presence of two pairs of cysteines, the first one located in the N-terminal part and the second at the C-terminal extremity that are probably involved in disulphide bonds. The best conserved region is located in the central part of these proteins [4-5].
Literature references
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Jacob-Dubuisson F, Striker R, Hultgren SJ;, J Biol Chem. 1994;269:12447-12455.: Chaperone-assisted self-assembly of pili independent of cellular energy. PUBMED:7909802 EPMC:7909802
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Schifferli DM, Alrutz MA;, J Bacteriol. 1994;176:1099-1110.: Permissive linker insertion sites in the outer membrane protein of 987P fimbriae of Escherichia coli. PUBMED:7906265 EPMC:7906265
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Van Rosmalen M, Saier MH Jr;, Res Microbiol. 1993;144:507-527.: Structural and evolutionary relationships between two families of bacterial extracytoplasmic chaperone proteins which function cooperatively in fimbrial assembly. PUBMED:7906046 EPMC:7906046
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Huang Y, Smith BS, Chen LX, Baxter RH, Deisenhofer J;, Proc Natl Acad Sci U S A. 2009;106:7403-7407.: Insights into pilus assembly and secretion from the structure and functional characterization of usher PapC. PUBMED:19380723 EPMC:19380723
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Remaut H, Tang C, Henderson NS, Pinkner JS, Wang T, Hultgren SJ, Thanassi DG, Waksman G, Li H;, Cell. 2008;133:640-652.: Fiber formation across the bacterial outer membrane by the chaperone/usher pathway. PUBMED:18485872 EPMC:18485872
Internal database links
SCOOP: | Big_6 |
Similarity to PfamA using HHSearch: | Usher_TcfC |
External database links
Transporter classification: | 1.B.11 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000015
In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two- component assembly and transport system which is composed of a periplasmic chaperone and an outer membrane protein which has been termed a molecular 'usher' [ PUBMED:7909802 , PUBMED:7906265 , PUBMED:7906046 ].
The usher protein is rather large (from 86 to 100kDa) and seems to be mainly composed of membrane-spanning beta-sheets, a structure reminiscent of porins. Although the degree of sequence similarity of these proteins is not very high, they share a number of characteristics. One of these is the presence of two pairs of cysteines, the first one located in the N-terminal part and the second at the C-terminal extremity that are probably involved in disulphide bonds. The best conserved region is located in the central part of these proteins [ PUBMED:19380723 , PUBMED:18485872 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | membrane (GO:0016020) |
Molecular function | fimbrial usher porin activity (GO:0015473) |
Biological process | pilus assembly (GO:0009297) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan MBB (CL0193), which has the following description:
This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.
The clan contains the following 100 members:
Ail_Lom Alginate_exp Autotransporter BBP2 BBP2_2 BBP7 BCSC_C Campylo_MOMP Caps_assemb_Wzi Channel_Tsx Chlam_OMP CopB CymA DcaP DUF2219 DUF2490 DUF2715 DUF2860 DUF3078 DUF3138 DUF3187 DUF3373 DUF3573 DUF3575 DUF4421 DUF4595 DUF481 DUF5020 DUF5777 DUF5916 DUF6048 DUF6089 DUF6268 Gcw_chp HP_OMP HP_OMP_2 HpuA IAT_beta KdgM LamB Legionella_OMP Lipoprot_C LptD LptD_2 MDM10 MipA MOSP_C MSP MtrB_PioB Omp85 Omp85_2 Omp_AT OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_like OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF PagL PagP Phenol_MetA_deg PLA1 Pom Porin_1 Porin_10 Porin_2 Porin_3 Porin_4 Porin_5 Porin_6 Porin_7 Porin_8 Porin_O_P Porin_OmpG Porin_OmpG_1_2 Porin_OmpL1 PorP_SprF PorV ShlB SlipAM Surface_Ag_2 TbpB_B_D TbpB_C Toluene_X TonB_dep_Rec TraF_2 TSA UPF0164 Usher Usher_TcfC YadA_anchor YaiO YfaZ YjbHAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (17) |
Full (1786) |
Representative proteomes | UniProt (48570) |
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RP15 (121) |
RP35 (602) |
RP55 (1794) |
RP75 (5388) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (17) |
Full (1786) |
Representative proteomes | UniProt (48570) |
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RP15 (121) |
RP35 (602) |
RP55 (1794) |
RP75 (5388) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | MRC-LMB Genome group and Prosite |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 17 |
Number in full: | 1786 |
Average length of the domain: | 448.80 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 63.96 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 549 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Usher domain has been found. There are 15 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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