VOLD_BPP2
ID VOLD_BPP2 Reviewed; 586 AA.
AC P13520;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1999, sequence version 2.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=Old nuclease {ECO:0000303|PubMed:7836278};
DE EC=3.1.11.3 {ECO:0000269|PubMed:7836278};
DE AltName: Full=Exodeoxyribonuclease Old {ECO:0000305};
DE AltName: Full=Overcoming lysogenization defect protein {ECO:0000303|PubMed:4884707};
DE Short=Old {ECO:0000303|PubMed:7836278};
GN Name=old {ECO:0000303|PubMed:4884707};
OS Escherichia phage P2 (Bacteriophage P2).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Myoviridae; Peduovirinae; Peduovirus.
OX NCBI_TaxID=10679;
OH NCBI_TaxID=543; Enterobacteriaceae.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2695400; DOI=10.1016/0378-1119(89)90460-5;
RA Haggaard-Ljungquist E., Barreiro V., Calendar R., Kurnit D.M., Cheng H.;
RT "The P2 phage old gene: sequence, transcription and translational
RT control.";
RL Gene 85:25-33(1989).
RN [2]
RP SEQUENCE REVISION TO 395.
RA Christie G.E., Haggard-Ljungquist E., Calendar R.;
RT "The complete genome of bacteriophage P2.";
RL Submitted (MAY-1998) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION.
RX PubMed=4884707; DOI=10.1016/0042-6822(69)90196-2;
RA Sironi G.;
RT "Mutants of Escherichia coli unable to be lysogenized by the temperate
RT bacteriophage P2.";
RL Virology 37:163-176(1969).
RN [4]
RP FUNCTION.
RX PubMed=4913204; DOI=10.1073/pnas.66.3.587;
RA Lindahl G., Sironi G., Bialy H., Calendar R.;
RT "Bacteriophage lambda; abortive infection of bacteria lysogenic for phage
RT P2.";
RL Proc. Natl. Acad. Sci. U.S.A. 66:587-594(1970).
RN [5]
RP FUNCTION AS AN EXONUCLEASE, CATALYTIC ACTIVITY, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=7836278; DOI=10.1128/jb.177.3.497-501.1995;
RA Myung H., Calendar R.;
RT "The old exonuclease of bacteriophage P2.";
RL J. Bacteriol. 177:497-501(1995).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, PROBABLE ACTIVE SITE, COFACTOR, AND
RP MUTAGENESIS OF LYS-37; ASP-299; HIS-306; HIS-332; GLU-398; GLU-402;
RP ASP-453; ASP-455; ASP-541; GLU-543 AND LYS-550.
RX PubMed=32009148; DOI=10.1093/nar/gkaa059;
RA Schiltz C.J., Adams M.C., Chappie J.S.;
RT "The full-length structure of Thermus scotoductus OLD defines the ATP
RT hydrolysis properties and catalytic mechanism of Class 1 OLD family
RT nucleases.";
RL Nucleic Acids Res. 48:2762-2776(2020).
CC -!- FUNCTION: An exonuclease that acts preferentially on linear dsDNA,
CC processively degrading it from 5'-3', releasing 5'-
CC phosphomononucleotides. Initiates on 5'-phosphate and 5'-hydroxyl ends.
CC Also acts on linear ssDNA, nicked DNA and RNA. ATP enhances but is not
CC necessary for exonuclease activity; has ATPase activity that is not
CC stimulated by DNA (PubMed:7836278). The old protein kills E.coli recB
CC and recC mutants and interferes with phage lambda growth
CC (PubMed:4913204). Both the exonuclease and ATPase activities are
CC required in vivo (PubMed:32009148). Probably interferes with lambda
CC phage by degrading its linear DNA (Probable). Isolated as a mutant able
CC to lysogenize E.coli strain C cells normally not susceptible to lysis
CC by phage P2 (PubMed:4884707). {ECO:0000269|PubMed:32009148,
CC ECO:0000269|PubMed:4884707, ECO:0000269|PubMed:4913204,
CC ECO:0000269|PubMed:7836278, ECO:0000305|PubMed:7836278}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage in the 5'- to 3'-direction to yield
CC nucleoside 5'-phosphates.; EC=3.1.11.3;
CC Evidence={ECO:0000269|PubMed:7836278};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:7836278};
CC Note=Mg(2+) gave the most activity in a maltose-binding protein fusion.
CC {ECO:0000269|PubMed:7836278};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7.2-8.8. {ECO:0000269|PubMed:7836278};
CC -!- SIMILARITY: Belongs to the class 1 OLD nuclease family.
CC {ECO:0000305|PubMed:32009148}.
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DR EMBL; AF063097; AAD03309.1; -; Genomic_DNA.
DR PIR; JQ0184; JQ0184.
DR RefSeq; NP_046798.1; NC_001895.1.
DR SMR; P13520; -.
DR GeneID; 1261523; -.
DR KEGG; vg:1261523; -.
DR Proteomes; UP000009092; Genome.
DR CDD; cd01026; TOPRIM_OLD; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR041685; AAA_15.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR034139; TOPRIM_OLD.
DR Pfam; PF13175; AAA_15; 2.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Exonuclease; Hydrolase; Metal-binding; Nuclease;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..586
FT /note="Old nuclease"
FT /id="PRO_0000165246"
FT REGION 1..163
FT /note="ATPase domain N-terminus"
FT /evidence="ECO:0000305|PubMed:32009148"
FT REGION 164..270
FT /note="Dimerization domain"
FT /evidence="ECO:0000305|PubMed:32009148"
FT REGION 271..390
FT /note="ATPase domain C-terminus"
FT /evidence="ECO:0000250|UniProtKB:E8PLM2"
FT REGION 393..586
FT /note="Toprim domain"
FT /evidence="ECO:0000303|PubMed:32009148"
FT ACT_SITE 570
FT /note="Stabilizes transition state or protonates leaving
FT group"
FT /evidence="ECO:0000305|PubMed:32009148"
FT BINDING 34..38
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:32009148"
FT BINDING 398
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000305|PubMed:32009148"
FT BINDING 402
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:32009148"
FT BINDING 453
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000305|PubMed:32009148"
FT BINDING 455
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000305|PubMed:32009148"
FT BINDING 541
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:32009148"
FT BINDING 543
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:32009148"
FT MUTAGEN 37
FT /note="K->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 299
FT /note="D->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 306
FT /note="H->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 332
FT /note="H->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 398
FT /note="E->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 402
FT /note="E->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 453
FT /note="D->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 455
FT /note="D->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 541
FT /note="D->A: No longer kills recB-recC deleted host cells,
FT viability is reduced."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 543
FT /note="E->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
FT MUTAGEN 550
FT /note="K->A: No longer kills recB-recC deleted host cells."
FT /evidence="ECO:0000269|PubMed:32009148"
SQ SEQUENCE 586 AA; 65381 MW; 4118550BDCA76F13 CRC64;
MTVRLASVSI SNFRSCKSTS AILRPFTALV GYNNAGKSNI ILAIKWLLDG SLISESDVYD
PTHPVSVEGV IQGITDDTLS LLTEENQQKI APFIIDGTLT FARRQEFNKE TGKAKKSLDV
YDGTTWKKNP GGIDGAISNI FPEPIHIPAM SDAVEDSTKC KNTTTIGKIL SAIVSEIKQE
HEEKFSKNIS EIGKYLSHNG ENRLESLNKI DSGVNKKVNQ FFPDVSVKLH FPTPTLDEIF
KSGTLKVFES REDEPVMRDI SRFGHGTQRS IQMALIQYLA EIKKENSESK KSNTLIFIDE
PELYLHPSAI NSVRESLVTL SESGYQVIIS THSASMLSAK HAANAIQVCK DSNGTIARKT
ISEKIEELYK SSSPQLHSAF TLSNSSYLLF SEEVLLVEGK TETNVLYALY KKINGHELNP
SKICIVAVDG KGSLFKMSQI INAIGIKTRI LADCDFLSNI LLTEHKDLLS TECDNLLTAL
IESINSGELS LNTKVTTFES FKSISSKDFI KICNHEKTQK HIHEIHQKLK DNGIYIWKSG
DIEAVYGFGK KQTEWDSLLD CLCDESKDVR AVIKKYDEME DFIKWI
