ID   RND_MUSP7               Reviewed;         374 AA.
AC   C6C608;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   27-JUL-2011, sequence version 2.
DT   25-MAY-2022, entry version 58.
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=Dd703_2009;
OS   Musicola paradisiaca (strain Ech703) (Dickeya paradisiaca) (Dickeya
OS   dadantii).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Pectobacteriaceae; Musicola.
OX   NCBI_TaxID=579405;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Ech703;
RG   US DOE Joint Genome Institute;
RA   Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA   Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C.,
RA   Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N.,
RA   Balakrishnan V., Glasner J., Perna N.T.;
RT   "Complete sequence of Dickeya dadantii Ech703.";
RL   Submitted (JUN-2009) 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}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=ACS85799.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; CP001654; ACS85799.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_023638302.1; NC_012880.1.
DR   AlphaFoldDB; C6C608; -.
DR   SMR; C6C608; -.
DR   STRING; 579405.Dd703_2009; -.
DR   EnsemblBacteria; ACS85799; ACS85799; Dd703_2009.
DR   KEGG; dda:Dd703_2009; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_1_6; -.
DR   Proteomes; UP000002734; 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..374
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411062"
FT   DOMAIN          3..171
FT                   /note="3'-5' exonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT   DOMAIN          210..289
FT                   /note="HRDC"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ   SEQUENCE   374 AA;  42472 MW;  1A4AA62DF8ADDE52 CRC64;
     MNYQLITTDD GLSEVCSQAR RMPQVALDTE FVRTRTYYPQ LGLIQLFDGE RLSLIDPLSI
     TVWQPFCDLL LDPAVTKYLH AGSEDLEVFL NAFGLLPTPF VDTQILVAFL GKPLSYGFAA
     LVADYMQVTL DKSESRTDWL ARPLSEKQCQ YAAADVYYLL PMAIRLVEET TSAGWWEAAL
     DECRQLCQRK QDVLAPEQAY REIGNAWQLK GRHLACLQKL ADWRLRKARE RDSAVNFIVR
     EEHLGQVARY LPGSLGELGA LGLSGPEIRY HGKTLLELVA ETQTMDAAEY PEPVINLIDY
     PGYKKAFREI KDLVQQQAER SGLSAELLAS RRQINRLLSW HWKLAPQTHV PELLSGWRGR
     LFGEPLKGIL ANYI