Protein Family Models

Date:

2024-08-14

SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [1, 2]. They are found in a great variety of intracellular or membrane-associated proteins [3, 4, 5] for example, in a variety of proteins with enzymatic activity, in adaptor proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes [6]. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region. Family members include probable invasion-associated protein p60 that are conceptually translated from iap genes. The iap gene, which is regarded as a virulence-associated gene in L. monocytogenes, codes for a gene product that has murein-lytic activity and is involved in cell division [7]. [1]. 15335710. SH2 and SH3. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

Most members of the NlpC/P60 family are lipoprotein-hydrolyzing enzymes, cleaving the D-gamma-glutamyl-meso-diaminopimelate linkage or N-acetylmuramate-l-alanine linkage. The family includes transglutaminases, papain-like cysteine peptidases, and arylamine acetyltransferases.

Date:

2024-10-16

EntFM (enterotoxin FM), originally described in Bacillus cereus strain FM-1, has repeated been shown to function as a toxin for eukaryotic cell lines, although the mechanism is not clearly described. The C-terminal region contains a NlpC/P60 domain, suggesting bacterial cell wall peptidase activity.

Gene:

entFM

Date:

2022-05-23

C40 family peptidase is a cell-wall hydrolase that cleaves peptide cross-bridges between glycan chains and is essential for bacterial growth and viability; typically cleaves the linkage between D-Glu and diaminopimelic acid (or Lys) within peptidoglycan stem peptides; contains a Cys-His-His catalytic triad

Date:

2022-08-18