ID   RND_ACICJ               Reviewed;         392 AA.
AC   A5G127;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   12-JUN-2007, sequence version 1.
DT   25-MAY-2022, entry version 68.
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=Acry_2365;
OS   Acidiphilium cryptum (strain JF-5).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales;
OC   Acetobacteraceae; Acidiphilium.
OX   NCBI_TaxID=349163;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=JF-5;
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., Dalin E., Tice H., Pitluck S.,
RA   Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Kyrpides N., Kim E., Magnuson T., Richardson P.;
RT   "Complete sequence of chromosome of Acidiphilium cryptum JF-5.";
RL   Submitted (MAY-2007) 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; CP000697; ABQ31559.1; -; Genomic_DNA.
DR   RefSeq; WP_012040004.1; NC_009484.1.
DR   AlphaFoldDB; A5G127; -.
DR   SMR; A5G127; -.
DR   STRING; 349163.Acry_2365; -.
DR   EnsemblBacteria; ABQ31559; ABQ31559; Acry_2365.
DR   KEGG; acr:Acry_2365; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_0_5; -.
DR   OMA; FMRVDTF; -.
DR   OrthoDB; 1462689at2; -.
DR   Proteomes; UP000000245; 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..392
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411058"
FT   DOMAIN          12..178
FT                   /note="3'-5' exonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT   DOMAIN          217..298
FT                   /note="HRDC"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ   SEQUENCE   392 AA;  42327 MW;  5868F32C1B95B59A CRC64;
     MKPSPSFPEP VLIETTEALA ALCDRLAAEP FVTVDTEFMR EKTYFPELCV VQLGGANDVA
     VIDAQAEGLD LAPLGALFAN PAVTKVFHAC RQDIEIFLLK FGAVPAPLFD TQVAAMVAGF
     GDQVGYDTLV SSLAGGRIDK AHRFSDWSAR PLSRAQIAYA AADVTWLRPV YEGLRARLTR
     EGRLDWVAEE AAVLADPATY RTEPEDAWRR LKLRGGNRRQ LALVKAIAAW REREAMRVNV
     PRQRIVRDEQ IPELAALAPA DAEGLTRVRG ISSGFAGGKS GRALLEVIAS TKAIPDAELP
     EAPRAPESAR PPAGLVALLK VLLAERAGAN HVAARLIASA EDIDRLASED APNLPCLQGW
     RAELFGNDAL RLKGGRIALA ARGRRVEVVD LP