ID   RND_SHESA               Reviewed;         388 AA.
AC   A0KXU5;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   12-DEC-2006, sequence version 1.
DT   25-MAY-2022, entry version 72.
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};
GN   OrderedLocusNames=Shewana3_2385;
OS   Shewanella sp. (strain ANA-3).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=94122;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ANA-3;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Chertkov O., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Newman D.,
RA   Salticov C., Konstantinidis K., Klappenback J., Tiedje J., Richardson P.;
RT   "Complete sequence of chromosome 1 of Shewanella sp. ANA-3.";
RL   Submitted (SEP-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; CP000469; ABK48614.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0KXU5; -.
DR   SMR; A0KXU5; -.
DR   STRING; 94122.Shewana3_2385; -.
DR   EnsemblBacteria; ABK48614; ABK48614; Shewana3_2385.
DR   KEGG; shn:Shewana3_2385; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_1_6; -.
DR   OMA; FMRVDTF; -.
DR   Proteomes; UP000002589; 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; -; 2.
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   SMART; SM00341; HRDC; 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; tRNA processing.
FT   CHAIN           1..388
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411072"
FT   DOMAIN          24..191
FT                   /note="3'-5' exonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT   DOMAIN          230..310
FT                   /note="HRDC"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ   SEQUENCE   388 AA;  44034 MW;  2C28F829E383813F CRC64;
     MSRLLFLWTV LNPQELEKNL SVFQYVSDEA SLNALVAQYQ QSPLLVLDTE FVRTRTYYAK
     LGLIQAYDGK TLALIDPVAL PDLSAFWSLL DNPNIIKLVH SCSEDLEVFA HYGQRQPTPL
     FDSQIAASLC GMGHGLGYAK LVETCLGEVI DKGESRTDWM RRPLTEAQLS YAANDVLYLY
     QLYPQLADKL KAQDRLGWLY EEGERMTEGR LATPDMDTAY LRVKNAFQLT EHQLAYLKVL
     AKWRLEKALA RDLALGFVIK DHGLIALAKK QPKSMGDLLK LNDLTEQEKR IHGKDILRVM
     QTADLSNPPE LVDVLALKPG YKSAFKNIKT CLSELCEQHA IPMEMLGSKR HIHEYLQWRW
     DKQQGELPTV LSGWRGQIAA ESLAKLDV