ID   RND_XANOR               Reviewed;         363 AA.
AC   Q5GZ75;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   27-JUL-2011, sequence version 2.
DT   25-MAY-2022, entry version 98.
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=XOO2742;
OS   Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC   Xanthomonadaceae; Xanthomonas.
OX   NCBI_TaxID=291331;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=KACC10331 / KXO85;
RX   PubMed=15673718; DOI=10.1093/nar/gki206;
RA   Lee B.-M., Park Y.-J., Park D.-S., Kang H.-W., Kim J.-G., Song E.-S.,
RA   Park I.-C., Yoon U.-H., Hahn J.-H., Koo B.-S., Lee G.-B., Kim H.,
RA   Park H.-S., Yoon K.-O., Kim J.-H., Jung C.-H., Koh N.-H., Seo J.-S.,
RA   Go S.-J.;
RT   "The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the
RT   bacterial blight pathogen of rice.";
RL   Nucleic Acids Res. 33:577-586(2005).
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=AAW75996.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; AE013598; AAW75996.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_041182166.1; NC_006834.1.
DR   AlphaFoldDB; Q5GZ75; -.
DR   SMR; Q5GZ75; -.
DR   STRING; 291331.XOO2742; -.
DR   EnsemblBacteria; AAW75996; AAW75996; XOO2742.
DR   KEGG; xoo:XOO2742; -.
DR   PATRIC; fig|291331.8.peg.3030; -.
DR   HOGENOM; CLU_042387_0_0_6; -.
DR   Proteomes; UP000006735; 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   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..363
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411074"
FT   DOMAIN          5..168
FT                   /note="3'-5' exonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT   DOMAIN          208..288
FT                   /note="HRDC"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ   SEQUENCE   363 AA;  40983 MW;  C5C7F58E54F08F03 CRC64;
     MPHWITHPSE LTDRLQAARP ARIGLDTEFI RERTYWPQLA LVQMAIGEEI LLIDPLIPGM
     NAALKEWLTA TDIVKVMHSA SEDLVTFKCA CGVLPRPLFD TQIAAALAGV GGGMGYQKLV
     QEVTGTLLTK GETRSDWMRR PLSPSQLEYA ADDVRYLFAI HDELTRRLTE QNRLGWLAED
     AERLLATVEH DDGERWPHVS LRTAQFLEPA AQRRLLRLLR WRDLQARQSD RPRSWILDNE
     VASQLARFPP ADLDALLQQF DKFPKAPRKL ANAVWDALNT PLPDEEHAPL AQAATDGNKA
     VLKRLQDTVA QRSHELGLPD GLLASRRHLE TLIEQRSWPA ALGQWRRAVL EAQVMPLLEA
     SEA