Protein Family Models

This HMM described a domain that is often repeated in pilins such as SpaA, and that often forms isopeptide bonds cross-linking amino acid side chains, giving the pilins added strength.

Date:

2024-10-16

GramPos_pilinD1 is the first subunit domain of Gram-positive pilins from Strep.pneumoniae. There are three major pilin subunits that form the polymeric backbone of the pilin from S. pneumoniae, constructed of three Ig-like, CnaB, domains along with a crucial N-terminal domain, D1. The three IG-like domains are stabilised by internal Lys-Asn isopeptide bonds, but this N-terminal domain makes few contact with the rest of the molecule due to the different orientation of its G beta-strand. Strand G of D1 also carries the YPKN motif that provides the essential Lys residue for the sortase-mediated intermolecular linkages along the pilus shaft. Gram-positive pili are formed from a single chain of covalently linked subunit proteins (pilins), usually comprising an adhesin at the distal tip, a major pilin that forms the polymer shaft and a minor pilin that mediates cell wall anchoring at the base [1]. [1]. 21760959. Structure of the full-length major pilin from Streptococcus pneumoniae: implications for isopeptide bond formation in gram-positive bacterial pili. Paterson NG, Baker EN;. PLoS One. 2011;6:e22095. (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

Members of this family are pilin major subunits whose structure includes an LPXTG motif-containing signal (see TIGR01167) near the C-terminus, for processing by sortases. Most contain a recognizable D2-type fimbrial isopeptide formation domain (see TIGR04226), in which Lys-to-Asn isopeptide bond formation provides additional structural integrity to support adhesion despite shear. For proper members of this subfamily, lengths fall typically in the range of 460 to 640 amino acids in length. Many members of this family contribute to the virulence of certain Gram-positive pathogens, including SpaA, SpaD, and SpaH from Corynebacterium diphtheriae, and EbpB and EbpC from Enterococcus faecalis.

Date:

2020-10-26

The Streptococcus Pneumoniae pilus backbone protein, RrgB, has three tandem domains with Lys-to-Asn isopeptide bonds, but these three regions are extremely divergent in sequence. This model represents the homology domain family of the D2 domain. It occurs just once in many surface proteins but up to twenty times in some pilin subunit proteins. Three of every four members have the typical Gram-positive C-terminal motif, LPXTG, although in many cases this motif may be involved in pilin subunit cross-linking rather than cell wall attachment. Proteins with this domain include fimbrial proteins with lectin-like adhesion functions, and the majority of characterized members are involved in surface adhesion to host structures.

Date:

2021-04-27

This model describes the LPXTG motif-containing region found at the C-terminus of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall. Hits that do not lie at the C-terminus or are not found in Gram-positive bacteria are probably false-positive. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.

Date:

2021-04-27