ID   RRP1_DROME              Reviewed;         679 AA.
AC   P27864; Q540Y1; Q9VQJ4;
DT   01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT   26-JUN-2007, sequence version 2.
DT   24-JAN-2024, entry version 181.
DE   RecName: Full=Recombination repair protein 1 {ECO:0000303|PubMed:1713691};
DE   AltName: Full=DNA-(apurinic or apyrimidinic site) endonuclease {ECO:0000250|UniProtKB:P27695};
DE            EC=3.1.11.2 {ECO:0000269|PubMed:16507570, ECO:0000269|PubMed:1713691, ECO:0000269|PubMed:8918793};
GN   Name=Rrp1 {ECO:0000303|PubMed:1713691,
GN   ECO:0000312|FlyBase:FBgn0004584};
GN   ORFNames=CG3178 {ECO:0000312|FlyBase:FBgn0004584};
OS   Drosophila melanogaster (Fruit fly).
OC   Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC   Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC   Drosophilidae; Drosophila; Sophophora.
OX   NCBI_TaxID=7227;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND
RP   SUBCELLULAR LOCATION.
RC   STRAIN=Oregon-R;
RX   PubMed=1713691; DOI=10.1073/pnas.88.15.6780;
RA   Sander M., Lowenhaupt K., Rich A.;
RT   "Drosophila Rrp1 protein: an apurinic endonuclease with homologous
RT   recombination activities.";
RL   Proc. Natl. Acad. Sci. U.S.A. 88:6780-6784(1991).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   STRAIN=Oregon-R;
RX   PubMed=1653418; DOI=10.1093/nar/19.16.4523;
RA   Sander M., Lowenhaupt K., Lane W.S., Rich A.;
RT   "Cloning and characterization of Rrp1, the gene encoding Drosophila strand
RT   transferase: carboxy-terminal homology to DNA repair endo/exonucleases.";
RL   Nucleic Acids Res. 19:4523-4529(1991).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=Canton-S;
RA   Tsoi S.C.M., Huang S.M., Sander M.;
RT   "Genomic organization of the Drosophila 23C genetic interval:
RT   identification of 3 genes in the 10Kb region surrounding the RRP1 gene.";
RL   Submitted (JUN-1998) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Berkeley;
RX   PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA   Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA   Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA   George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA   Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA   Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA   Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA   An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA   Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA   Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA   Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA   Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA   Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA   Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA   Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA   Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA   Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA   Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA   Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA   Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA   Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA   Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA   McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA   Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA   Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA   Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA   Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA   Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA   Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA   Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA   Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA   Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA   Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA   Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA   Venter J.C.;
RT   "The genome sequence of Drosophila melanogaster.";
RL   Science 287:2185-2195(2000).
RN   [5]
RP   GENOME REANNOTATION.
RC   STRAIN=Berkeley;
RX   PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA   Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA   Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA   Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA   Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA   Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA   Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT   "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT   review.";
RL   Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=Berkeley; TISSUE=Larva, and Pupae;
RX   PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
RA   Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A.,
RA   Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M.,
RA   Celniker S.E.;
RT   "A Drosophila full-length cDNA resource.";
RL   Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
RN   [7]
RP   FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND SUBCELLULAR LOCATION.
RX   PubMed=8918793; DOI=10.1093/nar/24.20.3926;
RA   Sander M., Benhaim D.;
RT   "Drosophila Rrp1 3'-exonuclease: demonstration of DNA sequence dependence
RT   and DNA strand specificity.";
RL   Nucleic Acids Res. 24:3926-3933(1996).
RN   [8]
RP   FUNCTION, CATALYTIC ACTIVITY, COFACTOR, INTERACTION WITH POLZ1 AND POLZ2,
RP   AND DEVELOPMENTAL STAGE.
RX   PubMed=16507570; DOI=10.1074/jbc.m512959200;
RA   Takeuchi R., Ruike T., Nakamura R., Shimanouchi K., Kanai Y., Abe Y.,
RA   Ihara A., Sakaguchi K.;
RT   "Drosophila DNA polymerase zeta interacts with recombination repair protein
RT   1, the Drosophila homologue of human abasic endonuclease 1.";
RL   J. Biol. Chem. 281:11577-11585(2006).
RN   [9]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-133; THR-140; SER-142 AND
RP   SER-258, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC   TISSUE=Embryo;
RX   PubMed=18327897; DOI=10.1021/pr700696a;
RA   Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P.;
RT   "Phosphoproteome analysis of Drosophila melanogaster embryos.";
RL   J. Proteome Res. 7:1675-1682(2008).
CC   -!- FUNCTION: Plays a role in the cellular response to oxidative stress by
CC       promoting DNA repair mechanisms such as base excision repair and
CC       possibly homologous recombination repair (PubMed:1713691,
CC       PubMed:16507570). Functions as an apurinic/apyrimidinic (AP)
CC       endodeoxyribonuclease in the DNA base excision repair (BER) pathway of
CC       DNA lesions induced by oxidative and alkylating agents
CC       (PubMed:16507570). Likely to initiate repair of AP sites in DNA by
CC       catalyzing hydrolytic incision of the phosphodiester backbone
CC       immediately adjacent to the damage, generating a single-strand break
CC       with 5'-deoxyribose phosphate and 3'-hydroxyl ends (By similarity). Has
CC       a 3'-5' exoribonuclease activity on mismatched deoxyribonucleotides at
CC       the 3' termini of nicked or gapped DNA molecules during short-patch BER
CC       (PubMed:16507570). Has apurinic endonuclease and double-stranded DNA
CC       3'-exonuclease activities and carries out single-stranded DNA
CC       renaturation in a Mg(2+)-dependent manner (PubMed:1713691,
CC       PubMed:8918793). Activity is more efficient in purine-rich regions of
CC       dsDNA than in pyrimidine-rich regions (PubMed:8918793).
CC       {ECO:0000250|UniProtKB:P27695, ECO:0000269|PubMed:16507570,
CC       ECO:0000269|PubMed:1713691, ECO:0000269|PubMed:8918793}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC         nucleoside 5'-phosphates.; EC=3.1.11.2;
CC         Evidence={ECO:0000269|PubMed:16507570, ECO:0000269|PubMed:1713691,
CC         ECO:0000269|PubMed:8918793};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:16507570, ECO:0000269|PubMed:1713691,
CC         ECO:0000269|PubMed:8918793};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000250|UniProtKB:P27695};
CC       Note=Probably binds two magnesium or manganese ions per subunit.
CC       {ECO:0000250|UniProtKB:P27695};
CC   -!- SUBUNIT: Interacts with the zeta DNA polymerase complex; interacts (via
CC       the N-terminus) with the accessory subunit PolZ2/Rev7 and also
CC       interacts with the catalytic component PolZ1, however the interaction
CC       with PolZ1 is likely via PolZ2. {ECO:0000269|PubMed:16507570}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00764,
CC       ECO:0000269|PubMed:1713691, ECO:0000269|PubMed:8918793}.
CC   -!- DEVELOPMENTAL STAGE: Expressed throughout development, with slightly
CC       higher levels of expression in 0-12 hour embryos and adult females.
CC       {ECO:0000269|PubMed:16507570}.
CC   -!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
CC       {ECO:0000305}.
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DR   EMBL; M62472; AAA62769.1; -; mRNA.
DR   EMBL; AF073994; AAC27621.1; -; Genomic_DNA.
DR   EMBL; AE014134; AAF51175.1; -; Genomic_DNA.
DR   EMBL; AY118605; AAM49974.1; -; mRNA.
DR   PIR; S28366; S28366.
DR   RefSeq; NP_476841.1; NM_057493.4.
DR   AlphaFoldDB; P27864; -.
DR   SMR; P27864; -.
DR   BioGRID; 59720; 3.
DR   IntAct; P27864; 2.
DR   STRING; 7227.FBpp0288680; -.
DR   iPTMnet; P27864; -.
DR   PaxDb; 7227-FBpp0288680; -.
DR   DNASU; 33500; -.
DR   EnsemblMetazoa; FBtr0077678; FBpp0077362; FBgn0004584.
DR   GeneID; 33500; -.
DR   KEGG; dme:Dmel_CG3178; -.
DR   AGR; FB:FBgn0004584; -.
DR   CTD; 8568; -.
DR   FlyBase; FBgn0004584; Rrp1.
DR   VEuPathDB; VectorBase:FBgn0004584; -.
DR   eggNOG; KOG1294; Eukaryota.
DR   eggNOG; KOG2992; Eukaryota.
DR   GeneTree; ENSGT00530000063540; -.
DR   InParanoid; P27864; -.
DR   PhylomeDB; P27864; -.
DR   Reactome; R-DME-110357; Displacement of DNA glycosylase by APEX1.
DR   Reactome; R-DME-110373; Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
DR   Reactome; R-DME-5651801; PCNA-Dependent Long Patch Base Excision Repair.
DR   Reactome; R-DME-73933; Resolution of Abasic Sites (AP sites).
DR   BioGRID-ORCS; 33500; 0 hits in 3 CRISPR screens.
DR   ChiTaRS; Rrp1; fly.
DR   GenomeRNAi; 33500; -.
DR   PRO; PR:P27864; -.
DR   Proteomes; UP000000803; Chromosome 2L.
DR   Bgee; FBgn0004584; Expressed in eye disc (Drosophila) and 51 other cell types or tissues.
DR   ExpressionAtlas; P27864; baseline and differential.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0008408; F:3'-5' exonuclease activity; IDA:FlyBase.
DR   GO; GO:0052720; F:class II DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:FlyBase.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0070182; F:DNA polymerase binding; IPI:FlyBase.
DR   GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:FlyBase.
DR   GO; GO:0008311; F:double-stranded DNA 3'-5' DNA exonuclease activity; IBA:GO_Central.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0008081; F:phosphoric diester hydrolase activity; IBA:GO_Central.
DR   GO; GO:0006284; P:base-excision repair; IBA:GO_Central.
DR   CDD; cd09087; Ape1-like_AP-endo; 1.
DR   Gene3D; 3.60.10.10; Endonuclease/exonuclease/phosphatase; 1.
DR   InterPro; IPR004808; AP_endonuc_1.
DR   InterPro; IPR020847; AP_endonuclease_F1_BS.
DR   InterPro; IPR020848; AP_endonuclease_F1_CS.
DR   InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR   InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR   NCBIfam; TIGR00195; exoDNase_III; 1.
DR   NCBIfam; TIGR00633; xth; 1.
DR   PANTHER; PTHR22748; AP ENDONUCLEASE; 1.
DR   PANTHER; PTHR22748:SF6; DNA-(APURINIC OR APYRIMIDINIC SITE) ENDONUCLEASE; 1.
DR   Pfam; PF03372; Exo_endo_phos; 1.
DR   SUPFAM; SSF56219; DNase I-like; 1.
DR   PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
DR   PROSITE; PS00727; AP_NUCLEASE_F1_2; 1.
DR   PROSITE; PS00728; AP_NUCLEASE_F1_3; 1.
DR   PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
DR   Genevisible; P27864; DM.
PE   1: Evidence at protein level;
KW   DNA damage; DNA repair; Hydrolase; Magnesium; Metal-binding; Nucleus;
KW   Phosphoprotein; Reference proteome.
FT   CHAIN           1..679
FT                   /note="Recombination repair protein 1"
FT                   /id="PRO_0000200017"
FT   REGION          1..407
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          428..679
FT                   /note="AP endonuclease"
FT   COMPBIAS        17..31
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        79..134
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        152..170
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        179..229
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        236..257
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        286..361
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        368..407
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        533
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        572
FT                   /note="Proton donor/acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         461
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         572
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         574
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         669
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   SITE            574
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000250"
FT   SITE            644
FT                   /note="Important for catalytic activity"
FT                   /evidence="ECO:0000250"
FT   SITE            670
FT                   /note="Interaction with DNA substrate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         133
FT                   /note="Phosphothreonine"
FT                   /evidence="ECO:0000269|PubMed:18327897"
FT   MOD_RES         140
FT                   /note="Phosphothreonine"
FT                   /evidence="ECO:0000269|PubMed:18327897"
FT   MOD_RES         142
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000269|PubMed:18327897"
FT   MOD_RES         258
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000269|PubMed:18327897"
FT   CONFLICT        76
FT                   /note="A -> V (in Ref. 1; no nucleotide entry, 2; AAA62769
FT                   and 3; AAC27621)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   679 AA;  74635 MW;  A05CC54A5A2C52DD CRC64;
     MPRVKAVKKQ AEALASEPTD PTPNANGNGV DENADSAAEE LKVPAKGKPR ARKATKTAVS
     AENSEEVEPQ KAPTAAARGK KKQPKDTDEN GQMEVVAKPK GRAKKATAEA EPEPKVDLPA
     GKATKPRAKK EPTPAPDEVT SSPPKGRAKA EKPTNAQAKG RKRKELPAEA NGGAEEAAEP
     PKQRARKEAV PTLKEQAEPG TISKEKVQKA ETAAKRARGT KRLADSEIAA ALDEPEVDEV
     PPKAASKRAK KGKMVEPSPE TVGDFQSVQE EVESPPKTAA APKKRAKKTT NGETAVELEP
     KTKAKPTKQR AKKEGKEPAP GKKQKKSADK ENGVVEEEAK PSTETKPAKG RKKAPVKAED
     VEDIEEAAEE SKPARGRKKA AAKAEEPDVD EESGSKTTKK AKKAETKTTV TLDKDAFALP
     ADKEFNLKIC SWNVAGLRAW LKKDGLQLID LEEPDIFCLQ ETKCANDQLP EEVTRLPGYH
     PYWLCMPGGY AGVAIYSKIM PIHVEYGIGN EEFDDVGRMI TAEYEKFYLI NVYVPNSGRK
     LVNLEPRMRW EKLFQAYVKK LDALKPVVIC GDMNVSHMPI DLENPKNNTK NAGFTQEERD
     KMTELLGLGF VDTFRHLYPD RKGAYTFWTY MANARARNVG WRLDYCLVSE RFVPKVVEHE
     IRSQCLGSDH CPITIFFNI
//