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14  structures 1526  species 0  interactions 8209  sequences 136  architectures

Family: Autotransporter (PF03797)

Summary: Autotransporter beta-domain

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This is the Wikipedia entry entitled "Autotransporter domain". More...

Autotransporter domain Edit Wikipedia article

Autotransporter beta-domain
PDB 1uyn EBI.jpg
Structure of the autotransporter domain NalP from Neisseria meningitidis. PDB entry 1uyn[1]
Identifiers
Symbol Autotransporter
Pfam PF03797
InterPro IPR005546
PROSITE PDOC51208
SCOP 1uyn
SUPERFAMILY 1uyn
TCDB 1.B.12
OPM superfamily 28
OPM protein 1uyo

In molecular biology, an autotransporter domain is a structural domain found in some bacterial outer membrane proteins. The domain is always located at the C-terminal end of the protein and forms a beta-barrel structure. The barrel is oriented in the membrane such that the N-terminal portion of the protein, termed the passenger domain, is presented on the cell surface. These proteins are typically virulence factors, associated with infection or virulence in pathogenic bacteria.

The name autotransporter derives from an initial understanding that the protein was self-sufficient in transporting the passenger domain through the outermembrane. This view has since been challenged by Benz and Schmidt.[2]

Secretion of polypeptide chains through the outer membrane of Gram-negative bacteria can occur via a number of different pathways. The type V(a), or autotransporter, secretion pathway constitutes the largest number of secreted virulence factors of any one of the seven known types of secretion in Gram-negative bacteria. This secretion pathway is exemplified by the prototypical IgA1 Protease of Neisseria gonorrhoeae.[3] The protein is directed to the inner membrane by a signal peptide transported across the inner membrane via the Sec machinery. Once in the periplasm, the autotransporter domain inserts into the outer membrane. The passenger domain is passed through the center of the autotransporter domain to be presented on the outside of the cell, however the mechanism by which this occurs remains unclear.[4]

The C-terminal translocator domain corresponds to an outer membrane beta-barrel domain. The N-terminal passenger domain is translocated across the membrane, and may or may not be cleaved from the translocator domain.[5] In those proteins where the cleavage is auto-catalytic, the peptidase domains belong to MEROPS peptidase families S6 and S8. Passenger domains structurally characterized to date have been shown to be dominated by a protein fold known as a beta helix, typified by pertactin. The folding of this domain is thought to be intrinsically linked to its method of outer membrane translocation.

See also[edit]

Trimeric Autotransporter Adhesins (TAA)

References[edit]

  1. ^ Oomen, C. J.; Van Ulsen, P.; Van Gelder, P.; Feijen, M.; Tommassen, J.; Gros, P. (2004). "Structure of the translocator domain of a bacterial autotransporter". The EMBO Journal 23 (6): 1257–1266. doi:10.1038/sj.emboj.7600148. PMC 381419. PMID 15014442. 
  2. ^ Benz, I.; Schmidt, M. A. (2011). "Structures and functions of autotransporter proteins in microbial pathogens". International Journal of Medical Microbiology 301 (6): 461–468. doi:10.1016/j.ijmm.2011.03.003. PMID 21616712.  edit
  3. ^ Pohlner, J.; Halter, R.; Beyreuther, K.; Meyer, T. F. (1987). "Gene structure and extracellular secretion of Neisseria gonorrhoeae IgA protease". Nature 325 (6103): 458–462. doi:10.1038/325458a0. PMID 3027577. 
  4. ^ Leo, J. C.; Grin, I.; Linke, D. (2012). "Type V secretion: Mechanism(s) of autotransport through the bacterial outer membrane". Philosophical Transactions of the Royal Society B: Biological Sciences 367 (1592): 1088–1101. doi:10.1098/rstb.2011.0208. PMC 3297439. PMID 22411980.  edit
  5. ^ Henderson, I. R.; Navarro-Garcia, F.; Nataro, J. P. (1998). "The great escape: Structure and function of the autotransporter proteins". Trends in microbiology 6 (9): 370–378. PMID 9778731. 

Further reading[edit]


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.

Autotransporter beta-domain Provide feedback

Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type V pathway was first described for the IgA1 protease [2]. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C terminus of the proteins it occurs in. The N terminus contains the variable passenger domain that is translocated across the membrane. Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different protease is used and in some cases no cleavage occurs [1].

Literature references

  1. Henderson IR, Navarro-Garcia F, Nataro JP; , Trends Microbiol 1998;6:370-378.: The great escape: structure and function of the autotransporter proteins. PUBMED:9778731 EPMC:9778731

  2. Pohlner J, Halter R, Beyreuther K, Meyer TF; , Nature 1987;325:458-462.: Gene structure and extracellular secretion of Neisseria gonorrhoeae IgA protease. PUBMED:3027577 EPMC:3027577

  3. Veiga E, Sugawara E, Nikaido H, de Lorenzo V, Fernandez LA; , EMBO J 2002;21:2122-2131.: Export of autotransported proteins proceeds through an oligomeric ring shaped by C-terminal domains. PUBMED:11980709 EPMC:11980709

  4. Oomen CJ, Van Ulsen P, Van Gelder P, Feijen M, Tommassen J, Gros P; , EMBO J 2004;23:1257-1266.: Structure of the translocator domain of a bacterial autotransporter. PUBMED:15014442 EPMC:15014442


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005546

Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type IV pathway was first described for the IgA1 protease [PUBMED:3027577]. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C terminus of the proteins it occurs in. The N terminus contains the variable passenger domain that is translocated across the membrane. Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different peptidase is used and in some cases no cleavage occurs [PUBMED:9778731]. In those proteins where the cleavage is auto-catalytic, the peptidase domains belong to MEROPS peptidase families S6 and S8.

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.

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(212)
Full
(8209)
Representative proteomes NCBI
(6497)
Meta
(851)
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(205)
RP35
(439)
RP55
(657)
RP75
(904)
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  Seed
(212)
Full
(8209)
Representative proteomes NCBI
(6497)
Meta
(851)
RP15
(205)
RP35
(439)
RP55
(657)
RP75
(904)
Alignment:
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  Seed
(212)
Full
(8209)
Representative proteomes NCBI
(6497)
Meta
(851)
RP15
(205)
RP35
(439)
RP55
(657)
RP75
(904)
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.

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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: [1]
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 212
Number in full: 8209
Average length of the domain: 238.90 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 26.88 %

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 22.0 20.8
Trusted cut-off 22.0 20.8
Noise cut-off 21.9 20.7
Model length: 265
Family (HMM) version: 14
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 Autotransporter domain has been found. There are 14 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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