Protein Family Models

This entry represents the domain I of NMB0315, an outer membrane protein of Neisseria meningitidis serogroup B and a potential candidate for a broad-spectrum vaccine against meningococcal disease. This domain tightly associates with domain III, which blocks the active site and the substrate binding groove [1]. Paper describing PDB structure 3slu. [1]. 22046377. Crystal structure of outer membrane protein NMB0315 from Neisseria meningitidis. Wang X, Yang X, Yang C, Wu Z, Xu H, Shen Y;. PLoS One. 2011;6:e26845. (from Pfam)

Date:

2024-10-16

This entry represents the second domain from the Csd3 peptidase [2]. This domain has a similar structure to Pfam:PF18059 despite low sequence similarity [2]. Paper describing PDB structure 2gu1. [1]. 18498110. Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae. Ragumani S, Kumaran D, Burley SK, Swaminathan S;. Proteins. 2008;72:1096-1103. Paper describing PDB structure 4rny. [2]. 25760614. Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase. An DR, Kim HS, Kim J, Im HN, Yoon HJ, Yoon JY, Jang JY, Hesek D, Lee M, Mobashery S, Kim SJ, Lee BI, Suh SW;. Acta Crystallogr D Biol Crystallogr. 2015;71:675-686. (from Pfam)

Date:

2024-10-16

This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [1,2]. This motif occurs at the N-terminus of these proteins. It contains a conserved histidine followed by a run of hydrophobic residues. [1]. 8559074. Identification and characterization of a cell envelope protein of Haemophilus influenzae contributing to phase variation in colony opacity and nasopharyngeal colonization. Weiser JN, Chong ST, Greenberg D, Fong W;. Mol Microbiol 1995;17:555-564. [2]. 8830271. Phenotypic switching of Haemophilus influenzae. Moxon ER, Gewurz BE, Richards JC, Inzana T, Jennings MP, Hood DW;. Mol Microbiol 1996;19:1149-1150. (from Pfam)

Date:

2024-10-16

The OapA domain gets its name from the Haemophilus influenzae protein OapA, which is required for the expression of colony opacity, thus opacity- associated protein A [1]. The OapA protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [1]. The OapA domain has been shown to bind to peptidoglycan in the E. coli protein YtfB [3]. A screen to identify factors that affect cell division in E. coli discovered that overproducing a fragment of YtfB, including its OapA domain, caused cells to grow as long filaments [3]. OapA domains are commonly associated with other domains that are involved in breaking peptidoglycan cross-links [4]. The OapA domain is distantly related to Pfam:PF01476. [1]. 8559074. Identification and characterization of a cell envelope protein of Haemophilus influenzae contributing to phase variation in colony opacity and nasopharyngeal colonization. Weiser JN, Chong ST, Greenberg D, Fong W;. Mol Microbiol 1995;17:555-564. [2]. 8830271. Phenotypic switching of Haemophilus influenzae. Moxon ER, Gewurz BE, Richards JC, Inzana T, Jennings MP, Hood DW;. Mol Microbiol 1996;19:1149-1150. [3]. 23565292. Harnessing single cell sorting to identify cell division genes and regulators in bacteria. Burke C, Liu M, Britton W, Triccas JA, Thomas T, Smith AL, Allen S, Salomon R, Harry E;. PLoS One. 2013;8:e60964. [4]. 29686141. YtfB, an OapA Domain-Containing Protein, Is a New Cell Division Protein in Escherichia coli. Jorgenson M. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation [1]. This domain may have a general peptidoglycan binding function. The structure of this domain is known [2]. [1]. 1352512. Modular design of the Enterococcus hirae muramidase-2 and Streptococcus faecalis autolysin. Joris B, Englebert S, Chu CP, Kariyama R, Daneo-Moore L, Shockman GD, Ghuysen JM;. FEMS Microbiol Lett 1992;70:257-264. [2]. 10843862. The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD). Bateman A, Bycroft M;. J Mol Biol 2000;299:1113-1119. (from Pfam)

Date:

2024-10-29

Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown. (from Pfam)

Date:

2024-08-14

Gene:

mepM

Date:

2021-09-22

murein DD-endopeptidase MepM is thought to cleave D-Ala-mDAP cross-links to allow insertion of new glycans and thus cell wall expansion

Date:

2019-07-15