ID   RND_JANSC               Reviewed;         386 AA.
AC   Q28RA7;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   04-APR-2006, sequence version 1.
DT   25-MAY-2022, entry version 76.
DE   RecName: Full=Ribonuclease D {ECO:0000255|HAMAP-Rule:MF_01899};
DE            Short=RNase D {ECO:0000255|HAMAP-Rule:MF_01899};
DE            EC=3.1.13.5 {ECO:0000255|HAMAP-Rule:MF_01899};
GN   Name=rnd {ECO:0000255|HAMAP-Rule:MF_01899}; OrderedLocusNames=Jann_1838;
OS   Jannaschia sp. (strain CCS1).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC   Roseobacteraceae; Jannaschia; unclassified Jannaschia.
OX   NCBI_TaxID=290400;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CCS1;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Pitluck S., Brettin T., Bruce D.,
RA   Han C., Tapia R., Gilna P., Chertkov O., Saunders E., Schmutz J.,
RA   Larimer F., Land M., Kyrpides N., Lykidis A., Moran M.A., Belas R., Ye W.,
RA   Buchan A., Gonzalez J.M., Schell M.A., Richardson P.;
RT   "Complete sequence of chromosome of Jannaschia sp. CCS1.";
RL   Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Exonuclease involved in the 3' processing of various
CC       precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA
CC       molecule and releases 5'-mononucleotides. {ECO:0000255|HAMAP-
CC       Rule:MF_01899}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Exonucleolytic cleavage that removes extra residues from the
CC         3'-terminus of tRNA to produce 5'-mononucleotides.; EC=3.1.13.5;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01899};
CC   -!- COFACTOR:
CC       Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01899};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01899}.
CC   -!- SIMILARITY: Belongs to the RNase D family. {ECO:0000255|HAMAP-
CC       Rule:MF_01899}.
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DR   EMBL; CP000264; ABD54755.1; -; Genomic_DNA.
DR   RefSeq; WP_011454960.1; NC_007802.1.
DR   AlphaFoldDB; Q28RA7; -.
DR   SMR; Q28RA7; -.
DR   STRING; 290400.Jann_1838; -.
DR   EnsemblBacteria; ABD54755; ABD54755; Jann_1838.
DR   KEGG; jan:Jann_1838; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_0_5; -.
DR   OMA; FMRVDTF; -.
DR   OrthoDB; 1462689at2; -.
DR   Proteomes; UP000008326; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0008408; F:3'-5' exonuclease activity; IEA:InterPro.
DR   GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR   GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR   GO; GO:0033890; F:ribonuclease D activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0042780; P:tRNA 3'-end processing; IEA:UniProtKB-UniRule.
DR   Gene3D; 1.10.150.80; -; 1.
DR   Gene3D; 3.30.420.10; -; 1.
DR   HAMAP; MF_01899; RNase_D; 1.
DR   InterPro; IPR002562; 3'-5'_exonuclease_dom.
DR   InterPro; IPR010997; HRDC-like_sf.
DR   InterPro; IPR002121; HRDC_dom.
DR   InterPro; IPR044876; HRDC_dom_sf.
DR   InterPro; IPR006292; RNase_D.
DR   InterPro; IPR012337; RNaseH-like_sf.
DR   InterPro; IPR036397; RNaseH_sf.
DR   Pfam; PF01612; DNA_pol_A_exo1; 1.
DR   Pfam; PF00570; HRDC; 1.
DR   SMART; SM00474; 35EXOc; 1.
DR   SUPFAM; SSF47819; SSF47819; 2.
DR   SUPFAM; SSF53098; SSF53098; 1.
DR   TIGRFAMs; TIGR01388; rnd; 1.
DR   PROSITE; PS50967; HRDC; 1.
PE   3: Inferred from homology;
KW   Cytoplasm; Exonuclease; Hydrolase; Nuclease; Reference proteome;
KW   tRNA processing.
FT   CHAIN           1..386
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411065"
FT   DOMAIN          3..174
FT                   /note="3'-5' exonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT   DOMAIN          213..294
FT                   /note="HRDC"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ   SEQUENCE   386 AA;  42398 MW;  89E9EF4C81B863BD CRC64;
     MPHTITTTDE LAAYCARAAT QPYVTVDTEF LRERTYFAQL CLVQVAMPGT DDTDAVLIDP
     LAEGLSLEPL YELFRNVNVV KVFHAARQDL EIFFVEGGLV PTPLFDTQVA AMVCGFGDQV
     GYETLVRRIA KANLDKSSRF TDWSRRPLSD AQKVYALADV TYLREIYEYL SAELARTDRT
     HWLEEELAQL TNADAYVVDP ENAWKRLKLR SNSGRVVAIA QQLAAFRETY AQEKNVPRNR
     VLKDDALLEL AGTKPKTVAD LGKSRLLLRD ARKGAIAEGL VAAVARGMSV PNSEIPKVQA
     GRDRSNLNPA LADLLRVLLK AKAENAGVAT KLIASSSDLD DIASGFTDGV WASGWRSEVF
     GADALRLLNG EVALAAKGQK VKIVEV