ID   RND_SPHJU               Reviewed;         388 AA.
AC   D4Z694;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   27-JUL-2011, sequence version 2.
DT   25-MAY-2022, entry version 57.
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=SJA_C1-32920;
OS   Sphingobium japonicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 /
OS   NBRC 101211 / UT26S).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC   Sphingomonadaceae; Sphingobium.
OX   NCBI_TaxID=452662;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S;
RX   PubMed=20817768; DOI=10.1128/jb.00961-10;
RA   Nagata Y., Ohtsubo Y., Endo R., Ichikawa N., Ankai A., Oguchi A., Fukui S.,
RA   Fujita N., Tsuda M.;
RT   "Complete genome sequence of the representative gamma-
RT   hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26.";
RL   J. Bacteriol. 192:5852-5853(2010).
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=BAI98126.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; AP010803; BAI98126.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_041386633.1; NC_014006.1.
DR   AlphaFoldDB; D4Z694; -.
DR   SMR; D4Z694; -.
DR   STRING; 452662.SJA_C1-32920; -.
DR   EnsemblBacteria; BAI98126; BAI98126; SJA_C1-32920.
DR   KEGG; sjp:SJA_C1-32920; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_0_5; -.
DR   Proteomes; UP000007753; Chromosome 1.
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..388
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411073"
FT   DOMAIN          7..173
FT                   /note="3'-5' exonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT   DOMAIN          212..293
FT                   /note="HRDC"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ   SEQUENCE   388 AA;  43562 MW;  9D688089414A11CE CRC64;
     MQIHPLITDS KTLAQFCARI AKSPYIAVDT EFMRENSYWP DLCLVQVADE HEAAAIDPKA
     PGLDLSPLLD LMVDNEDVLK VFHAGGQDLE IIYNLTGKTP HPLFDTQIAA MALGLGEQIG
     YGNLVDAWLG VQLDKGARFT DWARRPLDKR QIDYAIGDVT YLIQIFPKML EELRRTGRGD
     WLDQEMERIS DPSNYENKPE EAWQRVRIAS RKADVLGRLK ALAAWREMEA QDKNLPRGRI
     VKDETLADIA SHPPRTQEDL GKVRGLSATW KTNDIGNRLM LALASHAPLA KEEMPERDPK
     RPGLGKDGAL VADLLKLLLK IRSRDINVAA RLIARSDDID ALAAGVREDL AILEGWRYEQ
     FGRDAVDLVE GRLAFAVKNG RLKMTRTQ