ID   RND_ZYMMO               Reviewed;         390 AA.
AC   Q5NPM2;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-2005, sequence version 1.
DT   25-MAY-2022, entry version 88.
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=ZMO0714;
OS   Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC   Zymomonadaceae; Zymomonas.
OX   NCBI_TaxID=264203;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 31821 / ZM4 / CP4;
RX   PubMed=15592456; DOI=10.1038/nbt1045;
RA   Seo J.-S., Chong H., Park H.S., Yoon K.-O., Jung C., Kim J.J., Hong J.H.,
RA   Kim H., Kim J.-H., Kil J.-I., Park C.J., Oh H.-M., Lee J.-S., Jin S.-J.,
RA   Um H.-W., Lee H.-J., Oh S.-J., Kim J.Y., Kang H.L., Lee S.Y., Lee K.J.,
RA   Kang H.S.;
RT   "The genome sequence of the ethanologenic bacterium Zymomonas mobilis
RT   ZM4.";
RL   Nat. Biotechnol. 23:63-68(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}.
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DR   EMBL; AE008692; AAV89338.1; -; Genomic_DNA.
DR   RefSeq; WP_011240601.1; NZ_CP035711.1.
DR   AlphaFoldDB; Q5NPM2; -.
DR   SMR; Q5NPM2; -.
DR   STRING; 264203.ZMO0714; -.
DR   EnsemblBacteria; AAV89338; AAV89338; ZMO0714.
DR   GeneID; 58026535; -.
DR   KEGG; zmo:ZMO0714; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_0_5; -.
DR   OMA; FMRVDTF; -.
DR   OrthoDB; 1462689at2; -.
DR   Proteomes; UP000001173; 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   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..390
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411075"
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   390 AA;  43855 MW;  D39C9EF2C9A4698E CRC64;
     MQIHPLITDS ATLAALCSRL SRADFIAIDT EFIRENSYWP ELCLIQIADD KEAAAIDPLA
     PGLDMTPLTD LLVNNEDILK VFHAGGQDLE IILHHTGKMP FPLFDTQIAA MALGVGEQVG
     YSNLVERYLS IKLDKGARFT DWSHRPLDRR QLDYAIADVT HLATLFPMLL KELRDKGRGA
     WLDQEMERLA DPSQYINDPE KSWLRIRMPN RKADILGRLK ALAAWREIEA QNRNIPRGRI
     AKDETLADLA IHPPRRQSDL VKVRGLSGSW GSNDIGQRLM EAIENAEALR PEEIPQRNDR
     KLCIGKDGAM IADLLKLLLK MRARDAEVAA RLIAKSDDIE GIIAGERENN PVLTGWRYDI
     FGKEAIALIE GKMAFSVQKG KIAMTLIEKE