ID   RND_PARL1               Reviewed;         384 AA.
AC   A7HYE5;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   27-JUL-2011, sequence version 2.
DT   25-MAY-2022, entry version 69.
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=Plav_3324;
OS   Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Parvibaculaceae; Parvibaculum.
OX   NCBI_TaxID=402881;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DS-1 / DSM 13023 / NCIMB 13966;
RX   PubMed=22675581; DOI=10.4056/sigs.2215005;
RA   Schleheck D., Weiss M., Pitluck S., Bruce D., Land M.L., Han S.,
RA   Saunders E., Tapia R., Detter C., Brettin T., Han J., Woyke T., Goodwin L.,
RA   Pennacchio L., Nolan M., Cook A.M., Kjelleberg S., Thomas T.;
RT   "Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-
RT   1(T)).";
RL   Stand. Genomic Sci. 5:298-310(2011).
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=ABS64928.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; CP000774; ABS64928.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_041536094.1; NC_009719.1.
DR   AlphaFoldDB; A7HYE5; -.
DR   SMR; A7HYE5; -.
DR   STRING; 402881.Plav_3324; -.
DR   EnsemblBacteria; ABS64928; ABS64928; Plav_3324.
DR   KEGG; pla:Plav_3324; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_0_5; -.
DR   OrthoDB; 1462689at2; -.
DR   Proteomes; UP000006377; 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   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; Reference proteome;
KW   tRNA processing.
FT   CHAIN           1..384
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411068"
FT   DOMAIN          1..170
FT                   /note="3'-5' exonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT   DOMAIN          208..289
FT                   /note="HRDC"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ   SEQUENCE   384 AA;  42837 MW;  162E327046587FD4 CRC64;
     MEIITTNEAL RAACDRLSTA GFVTVDTEFM RDATFWPILC LIQLAGPSDE LIVDPLAPDL
     DLAPFYALMK NRNVVKVFHA ARQDIEIFCH EGKAIPDPLF DTQVAAMVCG FGDSVGYETL
     VRKLAGGSVD KSSRFTDWSR RPLSDKQLQY AMADVTYLRT IYEVLAKRLT HTKRAHWVAE
     EMAVLQDPET YAMRPENAWK RVKARFRGQR GLAVLVEVAA WRERQAQERD LPRSRVMKDD
     ALAEIATQIP RTISDLDGLR AVPKGFSNSR SAASLMEAVE RGLAMKEEDI PVVEGPEPLP
     PGIGPLVELL KVLLKIKCEE HDVAQKLVAN VADLELIAAH SEADVGALKG WRRELFGEDA
     LRLKRGELAI GVKGKRIVLI ETKR