ID   RPND_ECOLU              Reviewed;         306 AA.
AC   B7NGZ6;
DT   10-MAY-2017, integrated into UniProtKB/Swiss-Prot.
DT   10-FEB-2009, sequence version 1.
DT   25-MAY-2022, entry version 48.
DE   RecName: Full=Recombination-promoting nuclease RpnD {ECO:0000303|PubMed:28096446};
DE            EC=3.1.21.-;
GN   Name=rpnD {ECO:0000303|PubMed:28096446}; Synonyms=yjiP;
GN   OrderedLocusNames=ECUMN_4949;
OS   Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=585056;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=UMN026 / ExPEC;
RX   PubMed=19165319; DOI=10.1371/journal.pgen.1000344;
RA   Touchon M., Hoede C., Tenaillon O., Barbe V., Baeriswyl S., Bidet P.,
RA   Bingen E., Bonacorsi S., Bouchier C., Bouvet O., Calteau A., Chiapello H.,
RA   Clermont O., Cruveiller S., Danchin A., Diard M., Dossat C., Karoui M.E.,
RA   Frapy E., Garry L., Ghigo J.M., Gilles A.M., Johnson J., Le Bouguenec C.,
RA   Lescat M., Mangenot S., Martinez-Jehanne V., Matic I., Nassif X., Oztas S.,
RA   Petit M.A., Pichon C., Rouy Z., Ruf C.S., Schneider D., Tourret J.,
RA   Vacherie B., Vallenet D., Medigue C., Rocha E.P.C., Denamur E.;
RT   "Organised genome dynamics in the Escherichia coli species results in
RT   highly diverse adaptive paths.";
RL   PLoS Genet. 5:E1000344-E1000344(2009).
RN   [2]
RP   FUNCTION.
RC   STRAIN=K12;
RX   PubMed=26162088; DOI=10.1371/journal.pone.0130813;
RA   Kingston A.W., Roussel-Rossin C., Dupont C., Raleigh E.A.;
RT   "Novel recA-independent horizontal gene transfer in Escherichia coli K-
RT   12.";
RL   PLoS ONE 10:E0130813-E0130813(2015).
RN   [3]
RP   ERRATUM OF PUBMED:26162088.
RX   PubMed=26618540; DOI=10.1371/journal.pone.0143991;
RA   Kingston A.W., Roussel-Rossin C., Dupont C., Raleigh E.A.;
RT   "Correction: Novel recA-independent horizontal gene transfer in Escherichia
RT   coli K-12.";
RL   PLoS ONE 10:E0143991-E0143991(2015).
RN   [4]
RP   FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF 262-ARG--SER-306.
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       (Probable). Expression of a repaired protein increases the frequency of
CC       recA-independent recombination, but also decreases viability probably
CC       via DNA damage as measured by induction of the SOS repair response; in
CC       a RecA strain expression has no effect on viability but does induce the
CC       SOS repair response (PubMed:26162088, PubMed:26618540). RecA-
CC       independent DNA recombination leads to replacement of recipient genes
CC       with large segments of donor DNA rather than DNA addition to the donor
CC       strain; increased expression of RpnD leads to smaller replacement
CC       segments, suggesting this protein may play a role in generating
CC       crossover events (PubMed:26162088, PubMed:26618540). Upon expression
CC       enhances RecA-independent DNA recombination 4.7-fold, concomitantly
CC       reducing viability by 94% and inducing DNA damage (PubMed:28096446).
CC       May play a role in horizontal gene transfer (PubMed:26162088,
CC       PubMed:26618540, PubMed:28096446). {ECO:0000269|PubMed:26162088,
CC       ECO:0000269|PubMed:26618540, ECO:0000269|PubMed:28096446}.
CC   -!- DISRUPTION PHENOTYPE: A quadruple rpnA-rpnB-rpnC-rpnD deletion shows no
CC       change in basal RecA-independent recombination (PubMed:28096446).
CC       {ECO:0000269|PubMed:28096446}.
CC   -!- SIMILARITY: Belongs to the Rpn/YhgA-like nuclease family.
CC       {ECO:0000305}.
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DR   EMBL; CU928163; CAR16060.1; -; Genomic_DNA.
DR   RefSeq; WP_000181202.1; NC_011751.1.
DR   RefSeq; YP_002415527.1; NC_011751.1.
DR   AlphaFoldDB; B7NGZ6; -.
DR   SMR; B7NGZ6; -.
DR   STRING; 585056.ECUMN_4949; -.
DR   EnsemblBacteria; CAR16060; CAR16060; ECUMN_4949.
DR   KEGG; eum:ECUMN_4949; -.
DR   PATRIC; fig|585056.7.peg.5113; -.
DR   HOGENOM; CLU_059548_1_0_6; -.
DR   OMA; TRRMPHH; -.
DR   Proteomes; UP000007097; Chromosome.
DR   GO; GO:0004520; F:endodeoxyribonuclease activity; 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.
FT   CHAIN           1..306
FT                   /note="Recombination-promoting nuclease RpnD"
FT                   /id="PRO_0000439833"
FT   MUTAGEN         262..306
FT                   /note="Missing: 2.3-fold increase in recombination, 1.6-
FT                   fold decrease in viability."
FT                   /evidence="ECO:0000269|PubMed:28096446"
SQ   SEQUENCE   306 AA;  35887 MW;  097D4A10A87836DE CRC64;
     MTNFTTSTPH DALFKTFLTH PDTARDFMEI HLPKDLRELC DLDSLKLESA SFVDEKLRAL
     HSDILWSVKT REGDGYIYVV IEHQSREDIH MAFRLMRYSM AVMQRHIEHD KRQPLPLVIP
     MLFYHGSRSP YPWSLCWLDE FADPTTARKL YNAAFPLVDV TVVPDDEIVQ HRRVALLELI
     QKHIRQRDLM GLIDQLVVLL VTECANDSQI TALLNYILLT GDEARFNEFI SELTRRMPQH
     RERIMTIAER IHNDGYIKGE QRILRLLLQN GADPEWIQKI TGLSAEQMQA LRQPLPERER
     YSWLKS