Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Combined Automated Annotation using Multiple IEA Methods
UniProtKB entry P03681 (TERM_BPPH2), Primer terminal protein
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UniProt records a second FUNCTION for the terminal protein, hydrolysis of host peptidoglycans during virus entry, cited to PMID:14763988; this is the source of the hydrolase and virus-entry keywords and of four IEA GOA rows.
"Hydrolyzes host peptidoglycans during virus entry."
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The terminal protein is part of a DNA-gp3-gp16 complex, the curated basis for the viral terminase complex annotation.
"Part of a DNA-gp3-gp16 complex (PubMed:9086269)."
Site-directed mutagenesis in the DNA linking site of bacteriophage phi 29 terminal protein: isolation and characterization of a Ser232----Thr mutant.
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Changing the priming Ser-232 to threonine abolishes formation of the initiation complex while leaving the interactions with the DNA polymerase and with DNA intact, showing that the priming hydroxyl is the functional element and is highly specific.
"The mutant terminal protein has been purified to homogeneity and shown to be inactive in the formation of the initiation complex"
Temperature-sensitive mutants affected in DNA synthesis in phage phi29 of Bacillus subtilis.
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A survey of phi29 temperature-sensitive mutants identified the cistrons whose mutants fail to synthesise phage DNA; gene 3 is among the DNA-synthesis genes. Only the title could be quoted, as the cached record carries no abstract.
"Temperature-sensitive mutants affected in DNA synthesis in phage phi29 of Bacillus subtilis."
Factors involved in the initiation of phage phi 29 DNA replication in vitro: requirement of the gene 2 product for the formation of the protein p3-dAMP complex.
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Formation of the p3-dAMP initiation complex in vitro requires protein p3, the phi29 DNA-protein p3 template and a functional gene 2 product, but not the products of genes 5, 6 or 17.
"The formation of the initiation complex is completely dependent on the presence of a functional gene 2 product, in addition to protein p3 and phi29 DNA-protein p3 as template."
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The assay used extracts of Bacillus subtilis infected with phi29 mutants in the DNA-synthesis genes, including gene 3, which is what makes the annotation from this paper an IMP.
"extracts from B. subtilis infected with phi29 mutants in genes 2, 3, 5, 6 and 17, involved in DNA synthesis, have been used"
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Host DNA polymerase III, DNA gyrase and RNA polymerase inhibitors do not affect initiation, so the initiation reaction is carried out by phage proteins.
"suggesting that these proteins are not involved in the initiation of phi29 DNA replication"
Protein p3 is linked to the DNA of phage phi 29 through a phosphoester bond between serine and 5'-dAMP.
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The covalent protein-DNA linkage of phi29 is an O,5'-deoxyadenylyl-L-serine bond between protein p3 and the terminal 5'-dAMP of the genome.
"protein p3 is covalently linked to phi 29 DNA through a phosphoester bond between L-serine and 5'-dAMP"
Initiation of phage phi 29 DNA replication in vitro: formation of a covalent complex between the terminal protein, p3, and 5'-dAMP.
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A covalent complex between protein p3 and 5'-dAMP forms in extracts of phi29-infected Bacillus subtilis, identified by nuclease, phosphatase, RNase and proteinase K sensitivity and by piperidine release of 5'-dAMP.
"a covalent complex between protein p3 and 5'-dAMP is formed in vitro"
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The reaction depends on p3 and on the phi29 DNA-protein p3 template: it is blocked by anti-p3 serum and does not occur with proteinase K-treated phi29 DNA.
"was strongly inhibited by anti-p3 serum and required the preence of phi 29 DNA-protein p3 complex"
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The p3-dAMP initiation complex is a genuine primer: it is elongated on addition of dNTPs, and dideoxy-terminated products of 9 and 12 bases match the sequences at the left and right genome ends.
"can be elongated by addition of 40 microM dNTPs"
Bacillus subtilis phage phi29. Characterization of gene products and functions.
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Mutants in six phi29 genes, among them gene 3, fail to synthesise phage DNA.
"Mutants in six genes do not synthesize phage DNA."
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The paper matched protein products to ten of the seventeen phi29 cistrons, including the band corresponding to p3.
"The protein products of 10 out of the 17 cistrons detected in the genome of phage phi29 have been identified."
The bacteriophage phi29 packaging proteins supercoil the DNA ends.
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DNA with covalently bound terminal protein is more compact than gp3-free DNA, and the faster sedimentation requires gp3.
"the faster sedimentation was both gp3 and Mg2+-dependent"
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gp16 co-sediments with DNA-gp3 fragments, and the resulting DNA-gp3-gp16 complexes are the preferred packaging substrate in the defined in vitro system.
"cosedimented with the fast-sedimenting DNA-gp3 fragments, and the putative L-DNA-gp3-gp16 complexes were packaged preferentially into proheads in the defined in vitro system"
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gp3 and gp16 together supercoil the genome ends, apparently as a prerequisite for efficient interaction with the prohead.
"DNA-gp3 has a maturation pathway in which the packaging proteins gp3 and gp16 supercoil the DNA ends, probably as a prerequisite for efficient interaction with the prohead."
The RGD sequence in phage phi29 terminal protein is required for interaction with phi29 DNA polymerase.
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Mutations in the RGD motif at terminal protein residues 256-258 reduce TP-dAMP formation and impair heterodimer formation, so the motif serves the interaction with the viral DNA polymerase rather than any integrin-binding role.
"the RGD sequence present in phi29 TP is primarily involved in interaction with the viral DNA polymerase"
Compartmentalization of phage phi29 DNA replication: interaction between the primer terminal protein and the membrane-associated protein p1.
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The membrane-associated phi29 replication protein p1 interacts with the primer terminal protein, and excess truncated p1 interferes with formation of the TP-dAMP initiation complex, suggesting that the replisome attaches to a p1-based membrane structure.
"interfere with the in vitro formation of the TP.dAMP initiation complex in a reaction that depends on the efficient formation of a primer TP-phi29 DNA polymerase heterodimer"
Peptidoglycan hydrolytic activities associated with bacteriophage virions.
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This survey of virion-associated muralytic activities attributed the phi29 activity to the terminal protein gp3, and is the source of UniProt's peptidoglycan-hydrolase FUNCTION line and of four IEA GOA rows on P03681.
"lies in the terminal protein gp3"
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The authors note that for most phages in the survey the enzymatic species could not be identified definitively, the activity being assayed on whole virions.
"In most cases, the lack of genetic and structural characterization of the phage precludes making a definitive identification of the enzymatic protein species."
The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition.
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phi29 solves the primer problem by using a serine hydroxyl of the terminal protein to prime replication.
"The DNA polymerase of bacteriophage phi29 solves this problem by using a serine hydroxyl of terminal protein to prime replication."
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The 3.0 A structure resolves the three terminal protein domains: one making no contacts, one binding the polymerase, and the priming domain occupying the cleft that duplex DNA uses during elongation.
"The 3.0 A resolution structure shows one domain of terminal protein making no interactions, a second binding the polymerase and a third domain containing the priming serine occupying the same binding cleft in the polymerase as duplex DNA does during elongation."
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The heterodimer cannot accommodate upstream template DNA, which explains why initiation is restricted to the genome ends.
"this heterodimer of polymerase and terminal protein cannot accommodate upstream template DNA, thereby explaining its specificity for initiating DNA synthesis only at the ends of the bacteriophage genome"
Involvement of phage phi29 DNA polymerase and terminal protein subdomains in conferring specificity during initiation of protein-primed DNA replication.
Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail.
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The phi29 tail protein gp13 has separate lysozyme-like glycosidase and metallo-endopeptidase domains.
"whose structures resemble lysozyme-like enzymes and metallo-endopeptidases, respectively"
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gp13 is located at the distal end of the tail knob, where the phage meets the peptidoglycan layer.
"this enzyme is located at the distal end of the phi29 tail knob"
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gp13, not the terminal protein, is the tail-associated peptidoglycan-degrading enzyme that cleaves both the glycan backbone and the peptide cross-links during entry.
"gp13 functions as a tail-associated, peptidoglycan-degrading enzyme able to cleave both the polysaccharide backbone and peptide cross-links of the peptidoglycan cell wall"
DNA packaging motor assembly intermediate of bacteriophage phi29.
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The prohead/pRNA/gp16 packaging motor supercoils DNA-gp3, as gp16 alone does, so gp16 can assemble on the prohead before engaging DNA-gp3.
"The complex was capable of supercoiling DNA-gp3 as observed previously for gp16 alone"
Phage phi29 and Nf terminal protein-priming domain specifies the internal template nucleotide to initiate DNA replication.
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Swapping the priming domains of the phi29 and Nf terminal proteins shows that this domain determines which internal template nucleotide directs initiation, with the terminal nucleotides recovered by sliding back.
"we show that this domain is the main structural determinant that dictates the internal 3' nucleotide used as template during initiation"
Viral terminal protein directs early organization of phage DNA replication at the bacterial nucleoid.
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The terminal proteins of phi29 and PRD1 associate with the nucleoid of their respective bacterial hosts independently of any other phage-encoded protein.
"associate with the host bacterial nucleoid independently of other viral-encoded proteins"
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The N-terminal domain (residues 1-73) binds DNA sequence-independently and is what targets the terminal protein to the nucleoid.
"possesses sequence-independent DNA-binding capacity and is responsible for its nucleoid association"
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The terminal protein recruits the phage DNA polymerase to the bacterial nucleoid, organising the early replication machinery there.
"the TP recruits the phage DNA polymerase to the bacterial nucleoid"
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Parental terminal protein covalently attached to the injected genome also co-localises with the Bacillus subtilis nucleoid in the absence of priming TP, shown by immunofluorescence in cells infected with the sus3(91) mutant.
"the phage parental TP indeed colocalizes with the B. subtilis nucleoid in the absence of priming TP"
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Nucleoid tethering is not explained by any of the obvious nucleoid-associated proteins; no interaction with HBsu, SMC, ScpA or Noc was detected.
"TP and nucleoid-associated proteins HBsu, SMC, ScpA, or Noc was detected by yeast two-hybrid assays"
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Later in infection the terminal protein and the DNA polymerase move together onto helix-like paths in an MreB-dependent manner.
"both proteins later are redistributed to enlarged helix-like structures in an MreB cytoskeleton-dependent way"
Involvement of residues of the 29 terminal protein intermediate and priming domains in the formation of a stable and functional heterodimer with the replicative DNA polymerase.
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Initiation proceeds through a DNA polymerase/terminal protein heterodimer that recognises the genome-end origins and primes replication from the hydroxyl of Ser-232.
"the DNA polymerase forms a heterodimer with a free TP that recognizes the origins and initiates replication using as primer the hydroxyl group of TP residue Ser232"
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The polymerase catalyses the covalent bond between the initiator dAMP and Ser-232 of the priming terminal protein; the terminal protein supplies the hydroxyl, the polymerase the chemistry.
"the polymerase catalyses the formation of a covalent bond between the initiator dAMP and the hydroxyl group of Ser232 of the primer TP in the initiation reaction"
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Residues of the intermediate and priming domains (R158, R169, E191, D198, Y250, E252, Q253, R256) are needed for a stable and functional heterodimer and for the first steps of replication.
"substitution of these residues had an effect on either the stability of the TP/DNA polymerase complex"
Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages.
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The terminal proteins of phi29, Nf, PRD1, Bam35 and Cp-1 localise to the nucleus when expressed in mammalian cells; the phi29 NLS lies within residues 1-37. The cells used are not phi29's host.
"were found to localize to the nucleus when expressed in mammalian cells"
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Attaching phi29 terminal protein to the 5' ends of DNA enhances gene delivery into the eukaryotic nucleus, which is the applied significance of the NLS.
"gene delivery into the eukaryotic nucleus is enhanced by the presence of"
New insights in the ϕ29 terminal protein DNA-binding and host nucleoid localization functions.
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Mutating all the basic residues of the terminal protein N-terminal domain identifies the residues that bind the Bacillus subtilis genome and correlates DNA binding with nucleoid localisation.
"By mutating all the basic residues of the TP N-terminal domain we identify the amino acids responsible for its interaction with the"
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Those same residues are needed to recruit the DNA polymerase to the nucleoid and for efficient phage DNA replication.
"these residues are important to recruit the DNA polymerase at the bacterial nucleoid and, subsequently, for an efficient phage DNA replication"
Improved artificial origins for phage Phi29 terminal protein-primed replication. Insights into early replication events.
Dissecting the role of the ϕ29 terminal protein DNA binding residues in viral DNA replication.
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The N-terminal domain binds host DNA sequence-independently, and that binding is essential for nucleoid localisation and for efficient viral DNA replication in vivo; the DNA-binding residues also affect the Km of the polymerase for the initiating nucleotide.
"has been shown to bind to the host DNA in a sequence-independent manner and this binding is essential for the TP nucleoid localisation and for an efficient viral DNA replication in vivo"
Insights into the determination of the templating nucleotide at the initiation of phi29 DNA replication.