|
Holin Superfamily II
The Holin superfamily II is a superfamily of putative pore-forming proteins. It is one of the seven different holin superfamilies in total. In general, these proteins are thought to play a role in regulated cell death, although functionality varies between families and individual members. The Holin superfamily II includes the TC families: 1.E.1- The P21 Holin S (P21 Holin) Family 1.E.6- The T7 Holin (T7 Holin) Family 1.E.7- The HP1 Holin (HP1 Holin) Family 1.E.25- The ''Pseudomonas'' phage F116 Holin (F116 Holin) Family 1.E.50- The Beta-Proteobacterial Holin (BP-Hol) Family All four of these families are derived from Pseudomonadota and are of relatively small sizes, the average size of the proteins within the entire superfamily is 78 ± 14 amino acyl residues (aas). Some exceptions can be found (i.e., Lysis S family protein with 720 aasTC# 1.E.1.1.7. As in holin superfamily I, proteins in these families generally exhibit of 2 transmembrane spanners (TMSs). Families 1 and 6 i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Superfamily
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology (biology), homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent (due to low sequence similarity). Superfamilies typically contain several protein families which show sequence similarity within each family. The term ''protein clan'' is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems. Identification Superfamilies of proteins are identified using a number of methods. Closely related members can be identified by different methods to those needed to group the most evolutionarily divergent members. Sequence similarity Historically, the similarity of different amino acid sequences has been the most common method of inferring Sequence homology, h ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Integral Membrane Protein
An integral, or intrinsic, membrane protein (IMP) is a type of membrane protein that is permanently attached to the biological membrane. All ''transmembrane proteins'' are IMPs, but not all IMPs are transmembrane proteins. IMPs comprise a significant fraction of the proteins encoded in an organism's genome. Proteins that cross the membrane are surrounded by annular lipids, which are defined as lipids that are in direct contact with a membrane protein. Such proteins can only be separated from the membranes by using detergents, nonpolar solvents, or sometimes denaturing agents. Structure Three-dimensional structures of ~160 different integral membrane proteins have been determined at atomic resolution by X-ray crystallography or nuclear magnetic resonance spectroscopy. They are challenging subjects for study owing to the difficulties associated with extraction and crystallization. In addition, structures of many water-soluble protein domains of IMPs are available in the Prote ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Holin
Holins are a diverse group of small proteins produced by dsDNA bacteriophages in order to trigger and control the degradation of the host's cell wall at the end of the lytic cycle. Holins form pores in the host's cell membrane, allowing lysins to reach and degrade peptidoglycan, a component of bacterial cell walls. Holins have been shown to regulate the timing of lysis with great precision. Over 50 unrelated gene families encode holins, making them the most diverse group of proteins with common function. Together with lysins, holins are being studied for their potential use as antibacterial agents. While canonical holins act by forming large pores, pinholins such as the S protein of lambdoid phage 21 act by forming heptameric channels that depolarize the bacterial membrane. They are associated with SAR endolysins, which remain inactive in the periplasm prior to the depolarization of the membrane. Viruses that infect eukaryotic cells may use similar channel-forming proteins called ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cell Death
Cell death is the event of a biological cell ceasing to carry out its functions. This may be the result of the natural process of old cells dying and being replaced by new ones, as in programmed cell death, or may result from factors such as diseases, localized injury, or the death of the organism of which the cells are part. Apoptosis or Type I cell-death, and autophagy or Type II cell-death are both forms of programmed cell death, while necrosis is a non-physiological process that occurs as a result of infection or injury. Programmed cell death Programmed cell death (PCD) is cell death mediated by an intracellular program. PCD is carried out in a regulated process, which usually confers advantage during an organism's life-cycle. For example, the differentiation of fingers and toes in a developing human embryo occurs because cells between the fingers apoptose; the result is that the digits separate. PCD serves fundamental functions during both plant and metazoa (multicellula ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
P21 Holin Family
The Phage 21 S (P21 Holin) FamilyTC# 1.E.1 is a member of the Holin Superfamily II. The Bacteriophage P21 Lysis protein S holinTC# 1.E.1.1.1 is the prototype for class II holins. Lysis S proteins have two transmembrane segments (TMSs), with both the N- and C-termini on the cytoplasmic side of the inner membrane. TMS1 may be dispensable for function. A homologue of the P21 holin is the holin of bacteriophage H-19BTC# 1.E.1.1.3. The gene encoding it has been associated with the Shiga-like Toxin I gene in ''E. coli''. It may function in toxin export as has been proposed for the ''X. nematophila'' holin-1TC #1.E.2.1.4. A representative list of proteins belonging to the P21 holin family can be found in thTransporter Classification Database See also * Holin * Lysin Lysins, also known as endolysins or murein hydrolases, are hydrolytic enzymes produced by bacteriophages in order to cleave the host's cell wall during the final stage of the lytic cycle. Lysins are highly evolved enzy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
T7 Holin Family
The T7 Holin familyTC# 1.E.6 is a member of the Holin Superfamily II. Members of this family are predominantly found in '' Caudovirales'' and ''Pseudomonadota''. They typically have only 1 transmembrane segment (TMS) and vary from 60 to 130 amino acyl residues in length. A representative list of proteins belonging to this family can be found in thTransporter Classification Database See also * Holin * Lysin Lysins, also known as endolysins or murein hydrolases, are hydrolytic enzymes produced by bacteriophages in order to cleave the host's cell wall during the final stage of the lytic cycle. Lysins are highly evolved enzymes that are able to target ... * Transporter Classification Database Further reading * Hammerling, Michael J; Ellefson, Jared W; Boutz, Daniel R; Marcotte, Edward M; Ellington, Andrew D; Barrick, Jeffrey E"Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness"''Nature Chemical Biology'' 10 (3): 178–180. doi: 10.1038/nchembio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
HP1 Holin Family
The HP1 Holin (HP1 Holin) FamilyTC# 1.E.7) is a member of the Holin Superfamily II. Proteins in this family are typically found to contain two transmembrane segments (TMSs) and range between 70 and 80 amino acyl residues (aas) in length. A representative list of proteins belonging to the HP1 holin family can be found in thTransporter Classification Database The NucE proteinTC# 1.E.25.2.1 in '' Serratia marcescens'' shows homology to phage holin proteins involved in releasing lysozyme to the peptidoglycan of Gram-negative bacteria. The protein contains two characteristic transmembrane segments (TMSs) with a positively charged C-terminus. When the nucC operon carrying the nucEDC genes is placed in the ''Escherichia coli'' chromosome, NucE functions as a holin. Additionally, NucE can complement lysis-defective bacteriophage mutants to allow for plaque formation and release of phage. Although NucE can function as a holin it is not involved in the transport of nuclease, an extracellular ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pseudomonas Phage F116 Holin
The ''Pseudomonas'' phage F116 holin is a non-characterized holin homologous to one in '' Neisseria gonorrheae'' that has been characterized. This protein is the prototype of the ''Pseudomonas'' phage F116 holin (F116 Holin) familyTC# 1.E.25, which is a member of the Holin Superfamily II. Bioinformatic analysis of the genome sequence of ''N. gonorrhoeae'' revealed the presence of nine probable prophage islands. The genomic sequence of FA1090 identified five genomic regions (NgoPhi1 - 5) that are related to dsDNA lysogenic phage. The DNA sequences from NgoPhi1, NgoPhi2 and NgoPhi3 contained regions of identity. A region of NgoPhi2 showed high similarity with the '' Pseudomonas aeruginosa'' generalized transducing phage F116. NgoPhi1 and NgoPhi2 encode functionally active phages. The holin gene of NgoPhi1 (identical to that encoded by NgoPhi2), when expressed in ''E. coli'', could substitute for the phage lambda S gene. See also * Holin * Lysin Lysins, also known as endolysins ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BP Holin Family
The β-proteobacterial holin (BP-Hol) familyTC# 1.E.50 is a small family that includes members derived from a number of '' Burkholderia'' phage as well as a '' Poloromonas'' species. As of April 3, 2016, this family belongs to the Holin superfamily II. Members oSaier Bioinformatics Labat University of California, San Diego found that the BP-Hol family is most closely related to the T7 holin familyTC# 1.E.6. These proteins are of 60 to 110 amino acyl residues (aas) in length and exhibit 1 or 2 transmembrane segments (TMSs). Some are annotated as type II hollins and may be related to members of the T7 Holin familyTC# 1.E.6, although BP-Hol proteins remain functionally uncharacterized. A representative list of the proteins belonging to the BP-Hol family can be found in thTransporter Classification Database See also * Holin * Lysin Lysins, also known as endolysins or murein hydrolases, are hydrolytic enzymes produced by bacteriophages in order to cleave the host's cell wall duri ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pseudomonadota
Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of phyla in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. The phylum Proteobacteria includes a wide variety of pathogenic genera, such as ''Escherichia'', '' Salmonella'', ''Vibrio'', ''Yersinia'', ''Legionella'', and many others.Slonczewski JL, Foster JW, Foster E. Microbiology: An Evolving Science 5th Ed. WW Norton & Company; 2020. Others are free-living (nonparasitic) and include many of the bacteria responsible for nitrogen fixation. Carl Woese established this grouping in 1987, calling it informally the "purple bacteria and their relatives". Because of the great diversity of forms found in this group, it was later informally named Proteobacteria, after Proteus, a Greek god of the sea capable of assuming many different shapes (not after the Proteobacteria genus ''Proteus''). In 2021 the Internat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Holin Superfamily I
The Holin Superfamily I (aka the CDD phage holin1 superfamily) is a superfamily of integral membrane transport proteins. It is one of the seven different holin superfamilies in total. In general, these proteins are thought to play a role in regulated cell death, although functionality varies between families and individual members. Its main constituent is the Phi11 Holin (φ11 Holin) Family. This family is made up of over 270 putative pore-forming proteins, all from '' Bacillota''. On average, proteins belonging to the holin I superfamily are about 100 amino acyl residues (aas) in length, although a large size variation exists among proteins of this superfamily. There does not seem to be deviation from the standard two transmembrane segments that these proteins possess. See also * Holins * Lysin Lysins, also known as endolysins or murein hydrolases, are hydrolytic enzymes produced by bacteriophages in order to cleave the host's cell wall during the final stage of the lytic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Conserved Domain Database
The Conserved Domain Database (CDD) is a database of well-annotated multiple sequence alignment models and derived database search models, for ancient domains and full-length proteins. Philosophy Domains can be thought of as distinct functional and/or structural units of a protein. These two classifications coincide rather often, as a matter of fact, and what is found as an independently folding unit of a polypeptide chain also carries specific function. Domains are often identified as recurring (sequence or structure) units, which may exist in various contexts. In molecular evolution such domains may have been utilized as building blocks, and may have been recombined in different arrangements to modulate protein function. CDD defines conserved domains as recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis. The goal of the NCBI conserved domain curation project is to provide database users with insights into how patt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
