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10  structures 937  species 0  interactions 6892  sequences 21  architectures

Family: Usher (PF00577)

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
PDB 1zdv EBI.jpg
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 208
OPM protein 2vqi

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[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ 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
  6. ^ 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 PMID 21637253

This article incorporates text from the public domain Pfam and InterPro IPR000015

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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


External database links

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 (see PROSITEDOC) 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 100 kDa) 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.

Gene Ontology

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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 54 members:

Ail_Lom Autotransporter Bac_surface_Ag Campylo_MOMP Channel_Tsx CopB DUF1302 DUF1597 DUF2320 DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3374 DUF3575 DUF4289 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP MipA OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF OstA_C PagL Phenol_MetA_deg Porin_1 Porin_2 Porin_4 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ

Alignments

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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
(34)
Full
(6892)
Representative proteomes NCBI
(4642)
Meta
(66)
RP15
(58)
RP35
(144)
RP55
(319)
RP75
(466)
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Format an alignment

  Seed
(34)
Full
(6892)
Representative proteomes NCBI
(4642)
Meta
(66)
RP15
(58)
RP35
(144)
RP55
(319)
RP75
(466)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(34)
Full
(6892)
Representative proteomes NCBI
(4642)
Meta
(66)
RP15
(58)
RP35
(144)
RP55
(319)
RP75
(466)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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.

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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 View help on the curation process

Seed source: MRC-LMB Genome group and Prosite
Previous IDs: none
Type: Family
Author: Bateman A, Desvaux M, Eberhardt R
Number in seed: 34
Number in full: 6892
Average length of the domain: 502.70 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 67.01 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 18.9 18.9
Trusted cut-off 19.7 19.0
Noise cut-off 18.6 17.9
Model length: 552
Family (HMM) version: 15
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 10 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 seqence.

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