Gp17 from Siphoviridae bacteriophage SPP1 is a tail completion protein located at the interface between the connector protein gp16 and the tail of bacteriophage SPP1 []. Gp17 plays a fundamental role in the head-to-tail joining reaction, the ultimate step of virus particle assembly [].
The bacteriophage portal protein forms a gateway, or portal, enabling DNA passage during packaging and ejection of the phage genome. It also forms the junction between the phage head (capsid) and the tail proteins []. During SPP1 morphogenesis, Gp6 participates in the procapsid assembly reaction [, ].In the mature SPP1 virion, the portal protein, GP6, exists as a dodecamer, whereas recombinant SPP1 Gp6 has been shown to form 13-subunit assemblies [, ].This entry includes Bacillus phage SPP1-type portal proteins, Mycobacterium phage portal proteins and putative portal proteins of the Listeria phage A118-type.
This protein, also known as Gp17, protects the P22 phage from the superinfection exclusion system of other prophages, such as fels-2 [].Gp17 found in other bacteriophages such as SPP1 (siphophage SPP1, a lytic Bacillus subtilis phage) has been identified as a tail completion protein adopting an alpha/beta fold, and found to be located at the interface between the head-to-tail connector and the tail of bacteriophage SPP1 [].
This entry represents the N-terminal domain of Distal tail protein (Dit) from Bacillus phage SPP1 (Bacteriophage SPP1) and similar proteins found in bacteriophages and temperate phage of mainly from Firmicutes. This domain is approximately 125 amino acids long.Dit Forms a 40 Angstroms wide channel at the distal tip of the tail. It remains associated to the tail after DNA ejection [].
The portal protein is a bacteriophage component that forms a hole, or portal, enabling DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins [].This entry represents one particular subfamily of portal proteins consisting of the Bacillus phage SPP1 protein and similar sequences.
Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit [, ]. This entry represents the C-terminal domain of the large subunit.Proteins containing this domain include gp2 from Bacillus phage SPP1 [, ].
This family consists of several Siphovirus and other phage tail component proteins, including bacteriophage SPP1 distal tail protein Dit (also known as Gp19.1 or Gp19) [], as well as some bacterial proteins of unknown function. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
This domain is found in proteins found in the tailed bacteriophages Caudovirales and in bacterial prophages, internally or toward the C terminus.Minor head protein GP7 from Bacillus phage SPP1 is required for viral head morphogenesis []. Gp7 binds the viral DNA inside the capsid and the portal protein and may control the DNA exit from the virion []. Some other have also been identified as being involved in phage head morphogenesis [].
This group of sequences represent a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from the phage terminase family represented by .Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase are usually hetero-oligomers composed of a small and a large subunit [, ]. This entry includes the large subunit, including GP2 from Bacillus phage SPP1 [, ].
The COMPASS complex (complex proteins associated with Set1p) is conserved in yeasts and in other eukaryotes up to humans. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for the silencing of genes close to the telomeres of chromosomes []. Five domains are conserved in Saccharomyces cerevisiae Set1 and other eukaryotic Set1-related proteins: an amino-terminal RNA-recognition motif (RRM), a semi-conserved central domain, an N-SET domain, the catalytic SET domain, and the C-terminal post-SET domain. This entry represents the N-SET domain, which promotes trimethylation in conjunction with the RRM domain []and is necessary for binding of the Spp1 component of COMPASS into the complex [].
This entry describes the major tail protein (MTP) of the Siphoviridae and MTP genes in prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg9 (RCAP_rcc01691) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ]. The tail tube protein gp17.1* from bacteriophage SPP1 forms a sixfold helical, rigid tail tube which ejects of the phage DNA into the host when it binds to the entry receptor on the host cell surface, triggering structural rearrangements of the tail tube [].
This entry represents the N-terminal domain of the large subunit of the terminase protein.Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit. This region possess an endonuclease and ATPase activity that require Mg2+ and a neutral or slightly basic reaction. This region is also found in bacterial sequences [, ].Proteins containing this domain include gp2 from Bacillus phage SPP1 [, ].
Members of this family are associated with type VII secretion systems. EsaA from Staphylococcus aureus is encoded within a cluster comprised of eight predicted ORFs (esxA, esaA, essA, esaB, essB, essC, esxY, and esxB) []. Its function is unknown, though it is probably involved, with EsxA and EsxB, in the establishment of infection in the host. It is not necessary for the production and secretion of EsxA or EsxB []. Some members of this family, such as YueB from Bacillus subtilis, seem to act as membrane receptors for bacteriophage SPP1 [].In some proteins this entry represents the conserved N-terminal domain.
Many DNA viruses package their genomes in a reaction catalysed by a powerful DNA-packaging motor, a complex that consists of a dodecameric portal protein and a terminase that converts ATP hydrolysis into linear translation of DNA. The terminase is formed by a small subunit, which binds to packaging initiation sites to prepare for genome packaging, and a large subunit which has ATPase activity and binds directly to the portal protein. The small subunit is essential for binding to DNA and also activates the large subunit ATPase activity [, , ].This entry represents the terminase large subunit, an ATPase necessary for viral DNA translocation into empty capsids and it also acts as an endonuclease that cuts the viral genome to initiate and to end a packaging reaction. Included in this family is the terminase large subunit from Bacillus phage SPP1 []and related sequences.
This entry describes the head-tail adaptor protein of bacteriophage SPP1and related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg7 (RCAP_rcc01689) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [].In bacteriophage SPP1, the gp16 protein functions as a stopper, locking the viral DNA into the capsid. When the tail attachment binds to the entry receptor, gp16 opens by a diaphragm-like motion, allowing the genome to exit the capsid through the tail tube to the host cell. During virion assembly, gp16 functions as a docking platform to which the preassembled tail binds [].The SPP1 head-to-tail connector is composed of cyclical dodecamers of the portal protein gp6 and of the 2 head completion proteins gp15 and gp16 [].
Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site []. The small terminase protein is essential for the initial recognition of viral DNA and regulates the motor's ATPase and nuclease activities during DNA translocation []and for switching between viral DNA replication and packaging. DNA packaging in tailed bacteriophages and in evolutionarily related herpesviruses is controlled by a viral-encoded terminase. The terminase complex characterised in Bacillus subtilis bacteriophages SF6 and SPP1 consists of two proteins: G1P and G2P [, ].
Spp1 is a component of the COMPASS (Set1C) complex []. It promotes meiotic DNA double-strand break formation in promoters by tethering histone H3K4 methylation sites to chromosome axes []. This entry also includes CXXC-type zinc finger protein 1 (also known as CFP1) from animals [].CXXC-type zinc finger protein 1 (CXXC1 or CFP1) is a component of the SETD1 histone H3K4 methyltransferase complex. CXXC1 directs the complex to a chromatin region via its CXXC zinc finger with a specificity for a CpG unmethylated motif, particularly CpGG [, ].The COMPASS (Complex Proteins Associated with Set1 or Set1C) is the yeast homologue of the human MLL complex, which is required for mono-, di-, and trimethylation of lysine 4 of histone H3 []. It is required in telomeric transcriptional silencing []. The complex consists of Set1, Bre2, Spp1, Sdc1, Shg1, Swd1, Swd2, and Swd3 [, ].
This entry describes the head-tail adaptor protein of bacteriophage SPP1and related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg7 (RCAP_rcc01689) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [].In bacteriophage SPP1, the gp16 protein functions as a stopper, locking the viral DNA into the capsid. When the tail attachment binds to the entry receptor, gp16 opens by a diaphragm-like motion, allowing the genome to exit the capsid through the tail tube to the host cell. During virion assembly, gp16 functions as a docking platform to which the preassembled tail binds [].The SPP1 head-to-tail connector is composed of cyclical dodecamers of the portal protein gp6 and of the 2 head completion proteins gp15 and gp16 [].
Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site []. The small terminase protein is essential for the initial recognition of viral DNA and regulates the motor's ATPase and nuclease activities during DNA translocation []and for switching between viral DNA replication and packaging. DNA packaging in tailed bacteriophages and in evolutionarily related herpesviruses is controlled by a viral-encoded terminase. The terminase complex characterised in Bacillus subtilis bacteriophages SF6 and SPP1 consists of two proteins: G1P and G2P [, ].This entry represents the N-terminal domain of the terminase small subunit, which contains a HTH DNA-binding motif []. The first three helices of G1P form the typical helix-turn-helix DNA-binding motif, which is followed by a fourth helix. The fourth helix acts as a linker between the DNA-binding domain and the oligomerization domain [].
The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of ORC2, ORC6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both ORC1 and ORC5 bind ATP, although only ORC1 has ATPase activity []. The binding of ATP by ORC1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of ORC1 is involved in formation of the pre-RC [, , ]. ATP binding by ORC5 is crucial for the stability of ORC as a whole. Only the ORC1-5 subunits are required for origin binding; ORC6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that ORC2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 []and the N terminus mediates an interaction with the S-phase cyclin Clb5 [].
The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of ORC2, ORC6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both ORC1 and ORC5 bind ATP, although only ORC1 has ATPase activity []. The binding of ATP by ORC1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of ORC1 is involved in formation of the pre-RC [, , ]. ATP binding by ORC5 is crucial for the stability of ORC as a whole. Only the ORC1-5 subunits are required for origin binding; ORC6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that ORC2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 []and the N terminus mediates an interaction with the S-phase cyclin Clb5 [].
