Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 430  species 0  interactions 1349  sequences 3  architectures

Family: Ail_Lom (PF06316)

Summary: Enterobacterial Ail/Lom protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Virulence-related outer membrane protein family". More...

Virulence-related outer membrane protein family Edit Wikipedia article

Virulence-related OMP
1qj8 opm.png
Identifiers
Symbol Ail_Lom
Pfam PF06316
InterPro IPR000758
PROSITE PDOC00582
SCOP 1qj9
SUPERFAMILY 1qj9
OPM superfamily 26
OPM protein 1qj8

Virulence-related outer membrane proteins are expressed in Gram-negative bacteria and are essential to bacterial survival within macrophages and for eukaryotic cell invasion.

This family consists of several bacterial and phage Ail/Lom-like proteins. The Yersinia enterocolitica Ail protein is a known virulence factor. Proteins in this family are predicted to consist of eight transmembrane beta-sheets and four cell surface-exposed loops. It is thought that Ail directly promotes invasion and loop 2 contains an active site, perhaps a receptor-binding domain. The phage protein Lom is expressed during lysogeny, and encode host-cell envelope proteins. Lom is found in the bacterial outer membrane, and is homologous to virulence proteins of two other enterobacterial genera. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis.

Examples

Members of this group include:

  • PagC, required by Salmonella typhimurium for survival in macrophages and for virulence in mice[1]
  • Rck outer membrane protein of the S. typhimurium virulence plasmid[2]
  • Ail, a product of the Yersinia enterocolitica chromosome capable of mediating bacterial adherence to and invasion of epithelial cell lines[3]
  • OmpX from Escherichia coli that promotes adhesion to and entry into mammalian cells. It also has a role in the resistance against attack by the human complement system[4]
  • a Bacteriophage lambda outer membrane protein, Lom[5]

Structure

The crystal structure of OmpX from E. coli reveals that OmpX consists of an eight-stranded antiparallel all-next-neighbour beta barrel.[6] The structure shows two girdles of aromatic amino acid residues and a ribbon of nonpolar residues that attach to the membrane interior. The core of the barrel consists of an extended hydrogen bonding network of highly conserved residues. OmpX thus resembles an inverse micelle. The OmpX structure shows that the membrane-spanning part of the protein is much better conserved than the extracellular loops. Moreover, these loops form a protruding beta sheet, the edge of which presumably binds to external proteins. It is suggested that this type of binding promotes cell adhesion and invasion and helps defend against the complement system. Although OmpX has the same beta-sheet topology as the structurally related outer membrane protein A (OmpA) IPR000498, their barrels differ with respect to the shear numbers and internal hydrogen-bonding networks.

References

  1. ^ Miller SI (1991). "PhoP/PhoQ: macrophage-specific modulators of Salmonella virulence?". Mol. Microbiol. 5 (9): 2073–2078. doi:10.1111/j.1365-2958.1991.tb02135.x. PMID 1766380. 
  2. ^ Cirillo DM, Heffernan EJ, Wu L, Harwood J, Fierer J, Guiney DG (1996). "Identification of a domain in Rck, a product of the Salmonella typhimurium virulence plasmid, required for both serum resistance and cell invasion". Infect. Immun. 64 (6): 2019–2023. PMC 174031. PMID 8675302. 
  3. ^ Miller VL, Bliska JB, Falkow S (1990). "Nucleotide sequence of the Yersinia enterocolitica ail gene and characterization of the Ail protein product". J. Bacteriol. 172 (2): 1062–1069. PMC 208537. PMID 1688838. 
  4. ^ Tommassen J, Stoorvogel J, van Bussel MJ, van de Klundert JA (1991). "Molecular characterization of an Enterobacter cloacae outer membrane protein (OmpX)". J. Bacteriol. 173 (1): 156–160. PMC 207169. PMID 1987115. 
  5. ^ Pulkkinen WS, Miller SI (1991). "A Salmonella typhimurium virulence protein is similar to a Yersinia enterocolitica invasion protein and a bacteriophage lambda outer membrane protein". J. Bacteriol. 173 (1): 86–93. PMC 207160. PMID 1846140. 
  6. ^ Schulz GE, Vogt J (1999). "The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence". Structure 7 (10): 1301–1309. doi:10.1016/S0969-2126(00)80063-5. PMID 10545325. 

Further reading

  • Miller VL, Beer KB, Heusipp G, Young BM, Wachtel MR (September 2001). "Identification of regions of Ail required for the invasion and serum resistance phenotypes". Mol. Microbiol. 41 (5): 1053–62. PMID 11555286. 
  • Barondess JJ, Beckwith J (August 1990). "A bacterial virulence determinant encoded by lysogenic coliphage lambda". Nature 346 (6287): 871–4. doi:10.1038/346871a0. PMID 2144037. 

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.

Enterobacterial Ail/Lom protein Provide feedback

This family consists of several bacterial and phage Ail/Lom-like proteins. The Yersinia enterocolitica Ail protein is a known virulence factor. Proteins in this family are predicted to consist of eight transmembrane beta-sheets and four cell surface-exposed loops. It is thought that Ail directly promotes invasion and loop 2 contains an active site, perhaps a receptor-binding domain [1]. The phage protein Lom is expressed during lysogeny, and encode host-cell envelope proteins. Lom is found in the bacterial outer membrane, and is homologous to virulence proteins of two other enterobacterial genera. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis [2].

Literature references

  1. Miller VL, Beer KB, Heusipp G, Young BM, Wachtel MR; , Mol Microbiol 2001;41:1053-1062.: Identification of regions of Ail required for the invasion and serum resistance phenotypes. PUBMED:11555286 EPMC:11555286

  2. Barondess JJ, Beckwith J; , Nature 1990;346:871-874.: A bacterial virulence determinant encoded by lysogenic coliphage lambda. PUBMED:2144037 EPMC:2144037


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000758

Virulence-related outer membrane proteins are expressed in Gram-negative bacteria and are essential to bacterial survival within macrophages and for eukaryotic cell invasion. Members of this group include:
  • PagC, required by Salmonella typhimurium for survival in macrophages and for virulence in mice [PUBMED:1766380]
  • Rck outer membrane protein of the S. typhimurium virulence plasmid [PUBMED:8675302]
  • Ail, a product of the Yersinia enterocolitica chromosome capable of mediating bacterial adherence to and invasion of epithelial cell lines [PUBMED:1688838]
  • OmpX from Escherichia coli that promotes adhesion to and entry into mammalian cells. It also has a role in the resistance against attack by the human complement system [PUBMED:1987115]
  • a Bacteriophage lambda outer membrane protein, Lom [PUBMED:1846140]
  • The crystal structure of OmpX from E. coli reveals that OmpX consists of an eight-stranded antiparallel all-next-neighbour beta barrel [PUBMED:10545325]. The structure shows two girdles of aromatic amino acid residues and a ribbon of nonpolar residues that attach to the membrane interior. The core of the barrel consists of an extended hydrogen-bonding network of highly conserved residues. OmpX thus resembles an inverse micelle. The OmpX structure shows that the membrane-spanning part of the protein is much better conserved than the extracellular loops. Moreover, these loops form a protruding beta sheet, the edge of which presumably binds to external proteins. It is suggested that this type of binding promotes cell adhesion and invasion and helps defend against the complement system. Although OmpX has the same beta-sheet topology as the structurally related outer membrane protein A (OmpA) INTERPRO, their barrels differ with respect to the shear numbers and internal hydrogen-bonding networks.

    Gene Ontology

    The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

    Domain organisation

    Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

    Loading domain graphics...

    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

    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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

    View options

    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
    (2)
    Full
    (1349)
    Representative proteomes NCBI
    (1298)
    Meta
    (2)
    RP15
    (2)
    RP35
    (6)
    RP55
    (10)
    RP75
    (22)
    Jalview View  View  View  View  View  View  View  View 
    HTML View  View  View  View  View  View     
    PP/heatmap 1 View  View  View  View  View     
    Pfam viewer View  View             

    1Cannot generate PP/Heatmap alignments for seeds; no PP data available

    Key: ✓ available, x not generated, not available.

    Format an alignment

      Seed
    (2)
    Full
    (1349)
    Representative proteomes NCBI
    (1298)
    Meta
    (2)
    RP15
    (2)
    RP35
    (6)
    RP55
    (10)
    RP75
    (22)
    Alignment:
    Format:
    Order:
    Sequence:
    Gaps:
    Download/view:

    Download options

    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
    (2)
    Full
    (1349)
    Representative proteomes NCBI
    (1298)
    Meta
    (2)
    RP15
    (2)
    RP35
    (6)
    RP55
    (10)
    RP75
    (22)
    Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
    Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

    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.

    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 View help on the curation process

    Seed source: Pfam-B_12325 (release 9.0)
    Previous IDs: none
    Type: Family
    Author: Moxon SJ
    Number in seed: 2
    Number in full: 1349
    Average length of the domain: 177.20 aa
    Average identity of full alignment: 65 %
    Average coverage of the sequence by the domain: 97.07 %

    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 20.8 20.8
    Trusted cut-off 21.7 20.8
    Noise cut-off 20.0 20.7
    Model length: 199
    Family (HMM) version: 6
    Download: download the raw HMM for this family

    Species distribution

    Sunburst controls

    Show

    This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

    Loading sunburst data...

    Tree controls

    Hide

    The tree shows the occurrence of this domain across different species. More...

    Loading...

    Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.