Protein Family Models

This entry represents the autochaperone domain of type 1 (AC-1) in the Type Va Secretion System (T5aSS). Autotransporters (ATs) belong to a family of modular proteins secreted by the Type V, subtype a, secretion system (T5aSS) and considered as an important source of virulence factors in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria). The AC of type 1 with beta-fold appears as a prevalent and conserved structural element exclusively associated to beta-helical AT passenger [1]. [1]. 29375499. Identification of the Autochaperone Domain in the Type Va. Secretion System (T5aSS): Prevalent Feature of Autotransporters. with a beta-Helical Passenger.. Rojas-Lopez M, Zorgani MA, Kelley LA, Bailly X, Kajava AV,. Henderson IR, Polticelli F, Pizza M, Rosini R, Desvaux M;. Front Microbiol. 2018;8:2607. (from Pfam)

Date:

2024-08-14

This Autotransporter-associated beta strand repeat model represents a core 32-residue region of a class of bacterial protein repeat found in one to 30 copies per protein. Most proteins with a copy of this repeat have domains associated with membrane autotransporters (Pfam:PF03797). The repeats occur with a periodicity of 60 to 100 residues. A pattern of sequence conservation is that every second residue is well-conserved across most of the domain. These repeats as likely to have a beta-helical structure. This repeat plays a role in the efficient transport of autotransporter virulence factors to the bacterial surface during growth and infection. The repeat is always associated with the passenger domain of the autotransporter. For these reasons it has been coined the Passenger-associated Transport Repeat (PATR) [1]. The mechanism by which the PATR motif promotes transport is uncertain but it is likely that the conserved glycines (see HMM Logo) are required for flexibility of folding and that this folding drives secretion [1]. Autotransporters that contain PATR(s) associate with distinct virulence traits such as subtilisin (S8) type protease domains and polymorphic outer-membrane protein repeats, whilst SPATE (S6) type protease and lipase-like autotransporters do not tend to contain PATR motifs [1]. [1]. 25869731. The passenger-associated transport repeat promotes virulence. factor secretion efficiency and delineates a distinct. autotransporter subtype.. Doyle MT, Tran EN, Morona R;. Mol Microbiol. 2015; [Epub ahead of print] (from Pfam)

Date:

2024-08-14

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]. [1]. 9778731. The great escape: structure and function of the autotransporter. proteins.. Henderson IR, Navarro-Garcia F, Nataro JP;. Trends Microbiol 1998;6:370-378.. [2]. 3027577. Gene structure and extracellular secretion of Neisseria. gonorrhoeae IgA protease.. Pohlner J, Halter R, Beyreuther K, Meyer TF;. Nature 1987;325:458-462.. [3]. 11980709. Export of autotransported proteins proceeds through an. oligomeric ring shaped by C-terminal domains.. Veiga E, Sugawara E, Nikaido H, de Lorenzo V, Fernandez LA;. EMBO J 2002;21:2122-2131.. [4]. 15014442. Structure of the translocator domain of a bacterial. autotransporter.. Oomen CJ, Van Ulsen P, Van Gelder P, Feijen M, Tommassen J, Gros. P;. EMBO J 2004;23:1257-1266. (from Pfam)

Date:

2024-08-14

This family contains several Chlamydia polymorphic membrane proteins. Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract. Common for the Pmps are the tetrapeptide GGA(I/V/L) motif repeated several times in the N-terminal part. The C-terminal half is characterised by conserved tryptophans and a carboxy-terminal phenylalanine. A signal peptide leader sequence is predicted in 20 C. pneumoniae Pmps, which indicates an outer membrane localisation. Pmp10 and Pmp11 contain a signal peptidase II cleavage site suggesting lipid modification. The C. pneumoniae pmp genes represent 17.5% of the chlamydia-specific coding capacity and they are all transcribed during chlamydial growth but the function of Pmps remains unknown [1]. This family shows some similarity to Pfam:PF05594 and hence is likely to also form a beta-helical structure (personal obs:C Yeats). [1]. 11583841. Differential expression of Pmp10 in cell culture infected with. Chlamydia pneumoniae CWL029.. Pedersen AS, Christiansen G, Birkelund S;. FEMS Microbiol Lett 2001;203:153-159. (from Pfam)

Date:

2024-08-14

AIDA-I family autotransporter YfaL

Date:

2019-06-10

A number of Gram-negative bacterial proteins, mostly found in pathogens and associated with virulence, contain a conserved C-terminal domain that integrates into the outer membrane and enables the N-terminal region to be delivered across the membrane. This C-terminal autotransporter domain is about 400 amino acids in length and includes the aromatic amino acid-rich OMP signal, typically ending with a Phe or Trp residue, at the extreme C-terminus.

Date:

2024-06-21

This HMM represents a repeat region of about 27 residues that appears from twice to over twenty times in Chlamydial polymorphic outer membrane proteins (POMP). Characteristic motifs in the repeat are FXXN and GGAI. Except for a few apparently truncated examples, Chlamydial proteins have this repeat region if and only if they also have the autotransporter beta-domain (PF03797) at the C-terminus, with Phe as the C-terminal residue. This repeat is observed, but is very rare, outside the Chlamydias.

Date:

2021-07-01

This model represent a core 32-residue region of a class of bacterial protein repeat found in one to 30 copies per protein. Most proteins with a copy of this repeat have domains associated with membrane autotransporters (PF03797, TIGR01414). The repeats occur with a periodicity of 60 to 100 residues. A pattern of sequence conservation is that every second residue is well-conserved across most of the domain. Pfam model PF05594 is based on a longer, much more poorly conserved multiple sequence alignment and hits some of the same proteins as this model with some overlap between the hit regions of the two models. It describes these repeats as likely to have a beta-helical structure.

Date:

2020-10-23

The autotransporter adhesin YfaL, also called EhaC, is found in nearly all strains of Escherichia coli.

Gene:

yfaL

Date:

2021-10-04