RPNA_ECOLI
ID RPNA_ECOLI Reviewed; 292 AA.
AC P31667; Q2M776;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1993, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Recombination-promoting nuclease RpnA {ECO:0000303|PubMed:28096446};
DE EC=3.1.21.- {ECO:0000269|PubMed:28096446};
GN Name=rpnA {ECO:0000303|PubMed:28096446}; Synonyms=yhgA;
GN OrderedLocusNames=b3411, JW3374;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2678009; DOI=10.1093/nar/17.19.8004;
RA O'Regan M., Gloeckler R., Bernard S., Ledoux C., Ohsawa I., Lemoine Y.;
RT "Nucleotide sequence of the bioH gene of Escherichia coli.";
RL Nucleic Acids Res. 17:8004-8004(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=25316676; DOI=10.1093/bioinformatics/btu671;
RA Vlasblom J., Zuberi K., Rodriguez H., Arnold R., Gagarinova A., Deineko V.,
RA Kumar A., Leung E., Rizzolo K., Samanfar B., Chang L., Phanse S.,
RA Golshani A., Greenblatt J.F., Houry W.A., Emili A., Morris Q., Bader G.,
RA Babu M.;
RT "Novel function discovery with GeneMANIA: a new integrated resource for
RT gene function prediction in Escherichia coli.";
RL Bioinformatics 31:306-310(2015).
RN [5]
RP FUNCTION, COFACTOR, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES,
RP DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ASP-11; ASP-63; GLU-82; GLN-84;
RP ARG-94 AND ASP-165.
RC STRAIN=K12;
RX PubMed=28096446; DOI=10.1128/jb.00787-16;
RA Kingston A.W., Ponkratz C., Raleigh E.A.;
RT "The Rpn (YhgA-like) proteins of Escherichia coli K-12 and their
RT contribution to RecA-independent horizontal transfer.";
RL J. Bacteriol. 0:0-0(2017).
CC -!- FUNCTION: A low activity DNA endonuclease yielding 3'-hydroxyl ends,
CC equally active on ss or dsDNA, not active on dsRNA (PubMed:28096446).
CC Shows no sequence specificity (PubMed:28096446). Upon expression
CC enhances RecA-independent DNA recombination 49-fold, concomitantly
CC reducing viability by 88% and probably inducing DNA damage as measured
CC by induction of the SOS repair response in RecA cells
CC (PubMed:28096446). RecA-independent DNA recombination leads to
CC replacement of recipient genes with large segments of donor DNA rather
CC than DNA addition to the donor strain; increased expression of RpnA
CC leads to smaller replacement segments, suggesting this protein may play
CC a role in generating crossover events (PubMed:28096446).
CC {ECO:0000269|PubMed:28096446}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:28096446};
CC Note=Endonuclease activity partially supported by Mn(2+).
CC {ECO:0000269|PubMed:28096446};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA, Zn(2+) and by Mg(2+) plus
CC Mn(2+); stimulated by Ca(2+) in the presence of Mg(2+).
CC {ECO:0000269|PubMed:28096446}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 9.0, active between pH 7.5 and 10.5.
CC {ECO:0000269|PubMed:28096446};
CC -!- DISRUPTION PHENOTYPE: Cells grow to slightly higher density than wild-
CC type in sublethal levels of streptomycin (PubMed:25316676). A quadruple
CC rpnA-rpnB-rpnC-rpnD deletion shows no change in basal RecA-independent
CC recombination (PubMed:28096446). {ECO:0000269|PubMed:25316676,
CC ECO:0000269|PubMed:28096446}.
CC -!- SIMILARITY: Belongs to the Rpn/YhgA-like nuclease family.
CC {ECO:0000305}.
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DR EMBL; X15587; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U18997; AAA58209.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76436.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77880.1; -; Genomic_DNA.
DR PIR; F65136; F65136.
DR RefSeq; NP_417870.1; NC_000913.3.
DR RefSeq; WP_000039062.1; NZ_SSZK01000008.1.
DR AlphaFoldDB; P31667; -.
DR SMR; P31667; -.
DR BioGRID; 4263493; 9.
DR DIP; DIP-12335N; -.
DR IntAct; P31667; 1.
DR STRING; 511145.b3411; -.
DR PaxDb; P31667; -.
DR PRIDE; P31667; -.
DR EnsemblBacteria; AAC76436; AAC76436; b3411.
DR EnsemblBacteria; BAE77880; BAE77880; BAE77880.
DR GeneID; 947917; -.
DR KEGG; ecj:JW3374; -.
DR KEGG; eco:b3411; -.
DR PATRIC; fig|1411691.4.peg.3318; -.
DR EchoBASE; EB1700; -.
DR eggNOG; COG5464; Bacteria.
DR HOGENOM; CLU_059548_1_0_6; -.
DR InParanoid; P31667; -.
DR OMA; QEDIMTI; -.
DR PhylomeDB; P31667; -.
DR BioCyc; EcoCyc:EG11750-MON; -.
DR BioCyc; MetaCyc:EG11750-MON; -.
DR PRO; PR:P31667; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:1990238; F:double-stranded DNA endodeoxyribonuclease activity; IDA:EcoCyc.
DR GO; GO:0016888; F:endodeoxyribonuclease activity, producing 5'-phosphomonoesters; IDA:UniProtKB.
DR GO; GO:0006310; P:DNA recombination; IDA:UniProtKB.
DR InterPro; IPR010106; RpnA.
DR InterPro; IPR006842; Transposase_31.
DR Pfam; PF04754; Transposase_31; 1.
DR TIGRFAMs; TIGR01784; T_den_put_tspse; 1.
PE 1: Evidence at protein level;
KW DNA recombination; Endonuclease; Hydrolase; Magnesium; Nuclease;
KW Reference proteome.
FT CHAIN 1..292
FT /note="Recombination-promoting nuclease RpnA"
FT /id="PRO_0000169544"
FT MUTAGEN 11
FT /note="D->A: No longer increases recombination efficiency,
FT toxicity or SOS response."
FT /evidence="ECO:0000269|PubMed:28096446"
FT MUTAGEN 63
FT /note="D->A: No longer increases recombination efficiency,
FT toxicity or SOS response. No nuclease activity."
FT /evidence="ECO:0000269|PubMed:28096446"
FT MUTAGEN 82
FT /note="E->A: No longer increases recombination efficiency,
FT toxicity or SOS response."
FT /evidence="ECO:0000269|PubMed:28096446"
FT MUTAGEN 84
FT /note="Q->A: No longer increases recombination efficiency
FT or SOS response, more toxic than wild-type."
FT /evidence="ECO:0000269|PubMed:28096446"
FT MUTAGEN 84
FT /note="Q->K: No longer increases recombination efficiency,
FT toxicity or SOS response."
FT /evidence="ECO:0000269|PubMed:28096446"
FT MUTAGEN 94
FT /note="R->A: No longer increases recombination efficiency
FT or SOS response, more toxic than wild-type."
FT /evidence="ECO:0000269|PubMed:28096446"
FT MUTAGEN 165
FT /note="D->A: Hyperactive mutant, increases recombination
FT efficiency, more toxic than wild-type. Increased nuclease
FT activity."
FT /evidence="ECO:0000269|PubMed:28096446"
SQ SEQUENCE 292 AA; 33267 MW; FF3DF73DBBAF087E CRC64;
MSKKQSSTPH DALFKLFLRQ PDTARDFLAF HLPAPIHALC DMKTLKLESS SFIDDDLRES
YSDVLWSVKT EQGPGYIYCL IEHQSTSNKL IAFRMMRYAI AAMQNHLDAG YKTLPMVVPL
LFYHGIESPY PYSLCWLDCF ADPKLARQLY ASAFPLIDVT VMPDDEIMQH RRMALLELIQ
KHIRQRDLMG LVEQMACLLS SGYANDRQIK GLFNYILQTG DAVRFNDFID GVAERSPKHK
ESLMTIAERL RQEGEQSKAL HIAKIMLESG VPLADIMRFT GLSEEELAAA SQ
