TERM_BPPH2
ID TERM_BPPH2 Reviewed; 266 AA.
AC P03681; B3VMN7;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 21-JUL-1986, sequence version 1.
DT 29-SEP-2021, entry version 99.
DE RecName: Full=Primer terminal protein;
DE Short=TP;
DE AltName: Full=DNA terminal protein;
DE AltName: Full=Gene product 3;
DE Short=gp3;
DE AltName: Full=Protein p3;
DE AltName: Full=Terminal protein;
GN Name=3;
OS Bacillus phage phi29 (Bacteriophage phi-29).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Salasmaviridae; Picovirinae; Salasvirus.
OX NCBI_TaxID=10756;
OH NCBI_TaxID=1423; Bacillus subtilis.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6292852; DOI=10.1093/nar/10.19.5785;
RA Escarmis C., Salas M.;
RT "Nucleotide sequence of the early genes 3 and 4 of bacteriophage phi 29.";
RL Nucleic Acids Res. 10:5785-5798(1982).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6809534; DOI=10.1016/0378-1119(82)90149-4;
RA Yoshikawa H., Ito J.;
RT "Nucleotide sequence of the major early region of bacteriophage phi 29.";
RL Gene 17:323-335(1982).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Villegas A.P., Lingohr E.J., Ceyssens P.-J., Kropinski A.M.;
RL Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP IDENTIFICATION.
RX PubMed=416224; DOI=10.1016/0022-2836(78)90438-2;
RA Salas M., Mellado R.P., Vinuela E.;
RT "Characterization of a protein covalently linked to the 5' termini of the
RT DNA of Bacillus subtilis phage phi29.";
RL J. Mol. Biol. 119:269-291(1978).
RN [5]
RP COVALENT DNA LINKAGE AT SER-232.
RX PubMed=6779279; DOI=10.1073/pnas.77.11.6425;
RA Hermoso J.M., Salas M.;
RT "Protein p3 is linked to the DNA of phage phi 29 through a phosphoester
RT bond between serine and 5'-dAMP.";
RL Proc. Natl. Acad. Sci. U.S.A. 77:6425-6428(1980).
RN [6]
RP FUNCTION.
RX PubMed=6813861; DOI=10.1073/pnas.79.18.5522;
RA Penalva M.A., Salas M.;
RT "Initiation of phage phi 29 DNA replication in vitro: formation of a
RT covalent complex between the terminal protein, p3, and 5'-dAMP.";
RL Proc. Natl. Acad. Sci. U.S.A. 79:5522-5526(1982).
RN [7]
RP MUTAGENESIS OF SER-232.
RX PubMed=3135531; DOI=10.1093/nar/16.13.5727;
RA Garmendia C., Salas M., Hermoso J.M.;
RT "Site-directed mutagenesis in the DNA linking site of bacteriophage phi 29
RT terminal protein: isolation and characterization of a Ser232----Thr
RT mutant.";
RL Nucleic Acids Res. 16:5727-5740(1988).
RN [8]
RP IDENTIFICATION IN A DNA-GP3-GP16 COMPLEX.
RX PubMed=9086269; DOI=10.1006/jmbi.1996.0843;
RA Grimes S., Anderson D.;
RT "The bacteriophage phi29 packaging proteins supercoil the DNA ends.";
RL J. Mol. Biol. 266:901-914(1997).
RN [9]
RP MUTAGENESIS OF ARG-256; GLY-257 AND ASP-258.
RX PubMed=9705251; DOI=10.1006/viro.1998.9276;
RA Illana B., Zaballos A., Blanco L., Salas M.;
RT "The RGD sequence in phage phi29 terminal protein is required for
RT interaction with phi29 DNA polymerase.";
RL Virology 248:12-19(1998).
RN [10]
RP INTERACTION WITH THE REPLICATION PROTEIN P1.
RX PubMed=11032825; DOI=10.1093/emboj/19.20.5575;
RA Bravo A., Illana B., Salas M.;
RT "Compartmentalization of phage phi29 DNA replication: interaction between
RT the primer terminal protein and the membrane-associated protein p1.";
RL EMBO J. 19:5575-5584(2000).
RN [11]
RP FUNCTION.
RX PubMed=14763988; DOI=10.1046/j.1365-2958.2003.03894.x;
RA Moak M., Molineux I.J.;
RT "Peptidoglycan hydrolytic activities associated with bacteriophage
RT virions.";
RL Mol. Microbiol. 51:1169-1183(2004).
RN [12]
RP INTERACTION WITH THE DNA POLYMERASE.
RX PubMed=17913744; DOI=10.1093/nar/gkm749;
RA Perez-Arnaiz P., Longas E., Villar L., Lazaro J.M., Salas M., de Vega M.;
RT "Involvement of phage phi29 DNA polymerase and terminal protein subdomains
RT in conferring specificity during initiation of protein-primed DNA
RT replication.";
RL Nucleic Acids Res. 35:7061-7073(2007).
RN [13]
RP FUNCTION.
RX PubMed=18674782; DOI=10.1016/j.jmb.2008.04.034;
RA Koti J.S., Morais M.C., Rajagopal R., Owen B.A., McMurray C.T.,
RA Anderson D.L.;
RT "DNA packaging motor assembly intermediate of bacteriophage phi29.";
RL J. Mol. Biol. 381:1114-1132(2008).
RN [14]
RP FUNCTION.
RX PubMed=19011105; DOI=10.1073/pnas.0809882105;
RA Longas E., Villar L., Lazaro J.M., de Vega M., Salas M.;
RT "Phage phi29 and Nf terminal protein-priming domain specifies the internal
RT template nucleotide to initiate DNA replication.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:18290-18295(2008).
RN [15]
RP SUBCELLULAR LOCATION, AND FUNCTION.
RX PubMed=20823229; DOI=10.1073/pnas.1010530107;
RA Munoz-Espin D., Holguera I., Ballesteros-Plaza D., Carballido-Lopez R.,
RA Salas M.;
RT "Viral terminal protein directs early organization of phage DNA replication
RT at the bacterial nucleoid.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:16548-16553(2010).
RN [16]
RP FUNCTION, AND INTERACTION WITH VIRAL POLYMERASE.
RX PubMed=22210885; DOI=10.1093/nar/gkr1283;
RA del Prado A., Villar L., de Vega M., Salas M.;
RT "Involvement of residues of the Phi29 terminal protein intermediate and
RT priming domains in the formation of a stable and functional heterodimer
RT with the replicative DNA polymerase.";
RL Nucleic Acids Res. 40:3886-3897(2012).
RN [17]
RP SUBCELLULAR LOCATION, NUCLEAR LOCALIZATION SIGNAL, AND MUTAGENESIS OF
RP LYS-25 AND LYS-27.
RX PubMed=23091024; DOI=10.1073/pnas.1216635109;
RA Redrejo-Rodriguez M., Munoz-Espin D., Holguera I., Mencia M., Salas M.;
RT "Functional eukaryotic nuclear localization signals are widespread in
RT terminal proteins of bacteriophages.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:18482-18487(2012).
RN [18]
RP SUBCELLULAR LOCATION, AND MUTAGENESIS OF ARG-19; LYS-25 AND LYS-27.
RX PubMed=24205926; DOI=10.1111/mmi.12456;
RA Holguera I., Redrejo-Rodriguez M., Salas M., Munoz-Espin D.;
RT "New insights in the Phi29 terminal protein DNA-binding and host nucleoid
RT localization functions.";
RL Mol. Microbiol. 91:232-241(2014).
RN [19]
RP FUNCTION.
RX PubMed=25081208; DOI=10.1093/nar/gku660;
RA Gella P., Salas M., Mencia M.;
RT "Improved artificial origins for phage Phi29 terminal protein-primed
RT replication. Insights into early replication events.";
RL Nucleic Acids Res. 42:9792-9806(2014).
RN [20]
RP MUTAGENESIS OF PHE-227 AND PHE-230.
RX PubMed=26400085; DOI=10.1074/jbc.m115.682278;
RA del Prado A., Lazaro J.M., Longas E., Villar L., de Vega M., Salas M.;
RT "Insights into the determination of the templating nucleotide at the
RT initiation of phi29 DNA replication.";
RL J. Biol. Chem. 290:27138-27145(2015).
RN [21]
RP MUTAGENESIS OF ARG-19; LYS-25 AND LYS-27.
RX PubMed=25722367; DOI=10.1093/nar/gkv127;
RA Holguera I., Munoz-Espin D., Salas M.;
RT "Dissecting the role of the phi29 terminal protein DNA binding residues in
RT viral DNA replication.";
RL Nucleic Acids Res. 43:2790-2801(2015).
RN [22] {ECO:0007744|PDB:2EX3}
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 71-266.
RX PubMed=16511564; DOI=10.1038/sj.emboj.7601027;
RA Kamtekar S., Berman A.J., Wang J., Lazaro J.M., de Vega M., Blanco L.,
RA Salas M., Steitz T.A.;
RT "The phi29 DNA polymerase:protein-primer structure suggests a model for the
RT initiation to elongation transition.";
RL EMBO J. 25:1335-1343(2006).
CC -!- FUNCTION: Acts as a primer for DNA elongation during viral genomic
CC replication (PubMed:6813861). Acts as the small terminase protein
CC during packaging (PubMed:18674782). Recruits the phage DNA polymerase
CC to the bacterial nucleoid (PubMed:20823229). Primer terminal protein
CC (TP) is covalently linked to the 5'-ends of both strands of the genome
CC through a phosphodiester bond between the beta-hydroxyl group of a
CC serine residue and the 5'-phosphate of the terminal deoxyadenylate
CC (dAMP) (PubMed:6813861). To start replication, the DNA polymerase forms
CC a heterodimer with a free TP that recognizes the replication origins at
CC both 5' ends of the linear chromosome, and initiates replication using
CC as primer the OH-group of Ser-232 of the TP (PubMed:22210885,
CC PubMed:25081208). Since the polymerase initiates the replication on the
CC second thymine, the TP-dAMP initiation product slides backwards to
CC recover the template information of the first nucleotide
CC (PubMed:19011105). {ECO:0000269|PubMed:18674782,
CC ECO:0000269|PubMed:19011105, ECO:0000269|PubMed:20823229,
CC ECO:0000269|PubMed:22210885, ECO:0000269|PubMed:25081208,
CC ECO:0000269|PubMed:6813861}.
CC -!- FUNCTION: Hydrolyzes host peptidoglycans during virus entry.
CC {ECO:0000269|PubMed:14763988}.
CC -!- SUBUNIT: Interacts with the viral polymerase; this interaction allows
CC the initiation of TP-primed DNA replication at both viral DNA ends
CC (PubMed:22210885). Binds to ssDNA (PubMed:6779279). Interacts with the
CC replication protein p1 (PubMed:11032825). Part of a DNA-gp3-gp16
CC complex (PubMed:9086269). {ECO:0000269|PubMed:11032825,
CC ECO:0000269|PubMed:22210885, ECO:0000269|PubMed:6779279,
CC ECO:0000269|PubMed:9086269}.
CC -!- SUBCELLULAR LOCATION: Virion {ECO:0000269|PubMed:14763988}. Host
CC nucleus {ECO:0000269|PubMed:23091024}. Note=Associates with the host
CC bacterial nucleoid through its N-terminal region.
CC {ECO:0000269|PubMed:20823229}.
CC -!- SIMILARITY: Belongs to the phi29likevirus DNA terminal protein family.
CC {ECO:0000305}.
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DR EMBL; V01155; CAA24481.1; -; Genomic_DNA.
DR EMBL; J02479; AAA32290.1; -; Genomic_DNA.
DR EMBL; EU771092; ACE96024.1; -; Genomic_DNA.
DR PIR; A93439; ERBP39.
DR RefSeq; YP_002004530.1; NC_011048.1.
DR PDB; 2EX3; X-ray; 3.00 A; B/D/F/H/J/L=71-266.
DR PDBsum; 2EX3; -.
DR SMR; P03681; -.
DR GeneID; 6446514; -.
DR KEGG; vg:6446514; -.
DR EvolutionaryTrace; P03681; -.
DR Proteomes; UP000001207; Genome.
DR GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0043493; C:viral terminase complex; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0098932; P:disruption by virus of host cell wall peptidoglycan during virus entry; IEA:UniProtKB-KW.
DR GO; GO:0006269; P:DNA replication, synthesis of RNA primer; IEA:InterPro.
DR GO; GO:0018142; P:protein-DNA covalent cross-linking; IEA:InterPro.
DR GO; GO:0019073; P:viral DNA genome packaging; IDA:UniProtKB.
DR GO; GO:0039693; P:viral DNA genome replication; IDA:UniProtKB.
DR Gene3D; 1.20.1270.230; -; 1.
DR InterPro; IPR008770; DNA_terminal_Gp3.
DR InterPro; IPR043124; DNA_terminal_Gp3_C.
DR InterPro; IPR037216; DNA_terminal_Gp3_sf.
DR Pfam; PF05435; Phi-29_GP3; 1.
DR PIRSF; PIRSF004179; Phi-29_GP3; 1.
DR SUPFAM; SSF140919; SSF140919; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; Covalent protein-DNA linkage;
KW Degradation of host cell envelope components during virus entry;
KW Degradation of host peptidoglycans during virus entry; DNA replication;
KW DNA-binding; Early protein; Host nucleus; Hydrolase; Phosphoprotein;
KW Reference proteome; Viral DNA replication; Viral genome packaging;
KW Viral release from host cell; Virion; Virus entry into host cell.
FT CHAIN 1..266
FT /note="Primer terminal protein"
FT /id="PRO_0000106556"
FT REGION 1..73
FT /note="Disordered"
FT /evidence="ECO:0000269|PubMed:20823229"
FT REGION 74..172
FT /note="Intermediate; makes extensive contacts with the
FT phage DNA polymerase"
FT /evidence="ECO:0000269|PubMed:17913744"
FT REGION 173..266
FT /note="Priming"
FT /evidence="ECO:0000269|PubMed:16511564"
FT REGION 256..258
FT /note="Interaction with the viral DNA polymerase"
FT /evidence="ECO:0000269|PubMed:9705251"
FT COILED 86..113
FT /evidence="ECO:0000255"
FT MOTIF 25..34
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000269|PubMed:23091024"
FT SITE 230
FT /note="Positions the 3' end of the template strand at the
FT active site of the DNA polymerase"
FT /evidence="ECO:0000269|PubMed:26400085"
FT MOD_RES 232
FT /note="O-(5'-phospho-DNA)-serine"
FT /evidence="ECO:0000269|PubMed:6779279"
FT VARIANT 124..266
FT /note="Missing (in mutant SUS3(91))"
FT MUTAGEN 19
FT /note="R->A: No effect on TP-DNA amplification activity.
FT 60% loss of in vitro DNA-binding."
FT /evidence="ECO:0000269|PubMed:24205926,
FT ECO:0000269|PubMed:25722367"
FT MUTAGEN 25
FT /note="K->A: Loss of nuclear localization; when associated
FT with A-27."
FT /evidence="ECO:0000269|PubMed:23091024"
FT MUTAGEN 25
FT /note="K->A: No effect on TP-DNA amplification activity. No
FT effect on in vitro DNA-binding."
FT /evidence="ECO:0000269|PubMed:24205926,
FT ECO:0000269|PubMed:25722367"
FT MUTAGEN 27
FT /note="K->A: 88% loss of TP-DNA amplification activity. 80%
FT loss of in vitro DNA-binding. Impaired nucleoid
FT localization."
FT /evidence="ECO:0000269|PubMed:24205926,
FT ECO:0000269|PubMed:25722367"
FT MUTAGEN 27
FT /note="K->A: Loss of nuclear localization; when associated
FT with A-25."
FT /evidence="ECO:0000269|PubMed:23091024"
FT MUTAGEN 227
FT /note="F->V: No effect on the placement of the 3' terminus
FT of the template strand at the polymerization active site."
FT /evidence="ECO:0000269|PubMed:26400085"
FT MUTAGEN 230
FT /note="F->V: Formation of TP-dTMP is directed by the third
FT nucleotide of the template strand instead of the second."
FT /evidence="ECO:0000269|PubMed:26400085"
FT MUTAGEN 232
FT /note="S->T: Complete loss of priming activity."
FT /evidence="ECO:0000269|PubMed:3135531"
FT MUTAGEN 256
FT /note="R->K: 80% loss of primer activity."
FT /evidence="ECO:0000269|PubMed:9705251"
FT MUTAGEN 256
FT /note="R->M: 90% loss of primer activity."
FT /evidence="ECO:0000269|PubMed:9705251"
FT MUTAGEN 256
FT /note="R->T: 90% loss of primer activity."
FT /evidence="ECO:0000269|PubMed:9705251"
FT MUTAGEN 257
FT /note="G->A: 60% loss of primer activity."
FT /evidence="ECO:0000269|PubMed:9705251"
FT MUTAGEN 257
FT /note="G->D: 90% loss of primer activity."
FT /evidence="ECO:0000269|PubMed:9705251"
FT MUTAGEN 257
FT /note="G->V: 90% loss of primer activity."
FT /evidence="ECO:0000269|PubMed:9705251"
FT MUTAGEN 258
FT /note="D->E: 45% loss of primer activity."
FT /evidence="ECO:0000269|PubMed:9705251"
FT STRAND 77..79
FT /evidence="ECO:0007829|PDB:2EX3"
FT STRAND 85..87
FT /evidence="ECO:0007829|PDB:2EX3"
FT HELIX 88..112
FT /evidence="ECO:0007829|PDB:2EX3"
FT HELIX 115..118
FT /evidence="ECO:0007829|PDB:2EX3"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:2EX3"
FT HELIX 156..168
FT /evidence="ECO:0007829|PDB:2EX3"
FT HELIX 174..194
FT /evidence="ECO:0007829|PDB:2EX3"
FT HELIX 198..208
FT /evidence="ECO:0007829|PDB:2EX3"
FT HELIX 212..222
FT /evidence="ECO:0007829|PDB:2EX3"
FT TURN 223..225
FT /evidence="ECO:0007829|PDB:2EX3"
FT HELIX 237..255
FT /evidence="ECO:0007829|PDB:2EX3"
SQ SEQUENCE 266 AA; 31049 MW; 4C87B55670A48D65 CRC64;
MARSPRIRIK DNDKAEYARL VKNTKAKIAR TKKKYGVDLT AEIDIPDLDS FETRAQFNKW
KEQASSFTNR ANMRYQFEKN AYGVVASKAK IAEIERNTKE VQRLVDEKIK AMKDKEYYAG
GKPQGTIEQR IAMTSPAHVT GINRPHDFDF SKVRSYSRLR TLEESMEMRT DPQYYEKKMI
QLQLNFIKSV EGSFNSFDAA DELIEELKKI PPDDFYELFL RISEISFEEF DSEGNTVENV
EGNVYKILSY LEQYRRGDFD LSLKGF
