ID   RND_GRABC               Reviewed;         395 AA.
AC   Q0BVP4;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   27-JUL-2011, sequence version 2.
DT   25-MAY-2022, entry version 82.
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=GbCGDNIH1_0211;
OS   Granulibacter bethesdensis (strain ATCC BAA-1260 / CGDNIH1).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales;
OC   Acetobacteraceae; Granulibacter.
OX   NCBI_TaxID=391165;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-1260 / CGDNIH1;
RX   PubMed=17827295; DOI=10.1128/jb.00793-07;
RA   Greenberg D.E., Porcella S.F., Zelazny A.M., Virtaneva K., Sturdevant D.E.,
RA   Kupko J.J. III, Barbian K.D., Babar A., Dorward D.W., Holland S.M.;
RT   "Genome sequence analysis of the emerging human pathogenic acetic acid
RT   bacterium Granulibacter bethesdensis.";
RL   J. Bacteriol. 189:8727-8736(2007).
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=ABI61109.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; CP000394; ABI61109.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_043452603.1; NC_008343.2.
DR   AlphaFoldDB; Q0BVP4; -.
DR   SMR; Q0BVP4; -.
DR   STRING; 391165.GbCGDNIH1_0211; -.
DR   PRIDE; Q0BVP4; -.
DR   EnsemblBacteria; ABI61109; ABI61109; GbCGDNIH1_0211.
DR   KEGG; gbe:GbCGDNIH1_0211; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_0_5; -.
DR   Proteomes; UP000001963; 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..395
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411064"
FT   DOMAIN          14..181
FT                   /note="3'-5' exonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT   DOMAIN          219..300
FT                   /note="HRDC"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ   SEQUENCE   395 AA;  43449 MW;  DAE36D9A693D9304 CRC64;
     MSRQSRSRFP SPTLITKSED LAALCTTLRR EPYVTIDTEF MRERTYWPEL CVVQLGGADC
     VAVIDTLAPE LDLAPVGELL ADPAVIKVFH ACRQDIEIFL LRFGSIPQPM FDTQVAAMVA
     GFGDQVGYDT LVSSLTGGHI DKAHRFSDWS RRPLSQAQID YAAADVTHLR GVYETLRDRL
     EKEGRLAWVS EEMAVLNDPA TYRTDPVTMW ERLRPRTNNR RYLGLLRAIC AWREVEAQRL
     NIPRQRLIKD ESLLEIAATS PADAESLAQA RGVGRGFAEG RSGATLLAAI AEARGLPDAD
     LPAIPRSRES GARPSPALVS LLKVLLAAKS EQHNVAPKLL ASSEDLDRLA TEAEPDVPAL
     TGWRRDVFGQ DALALKNGEI CLGVDGKQIK LITTG