ID   RND_METSB               Reviewed;         399 AA.
AC   B8EN54;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   27-JUL-2011, sequence version 2.
DT   25-MAY-2022, entry version 62.
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=Msil_0208;
OS   Methylocella silvestris (strain DSM 15510 / CIP 108128 / LMG 27833 / NCIMB
OS   13906 / BL2).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Beijerinckiaceae; Methylocella.
OX   NCBI_TaxID=395965;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 15510 / CIP 108128 / LMG 27833 / NCIMB 13906 / BL2;
RX   PubMed=20472789; DOI=10.1128/jb.00506-10;
RA   Chen Y., Crombie A., Rahman M.T., Dedysh S.N., Liesack W., Stott M.B.,
RA   Alam M., Theisen A.R., Murrell J.C., Dunfield P.F.;
RT   "Complete genome sequence of the aerobic facultative methanotroph
RT   Methylocella silvestris BL2.";
RL   J. Bacteriol. 192:3840-3841(2010).
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=ACK49189.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; CP001280; ACK49189.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_041367441.1; NC_011666.1.
DR   AlphaFoldDB; B8EN54; -.
DR   SMR; B8EN54; -.
DR   STRING; 395965.Msil_0208; -.
DR   EnsemblBacteria; ACK49189; ACK49189; Msil_0208.
DR   KEGG; msl:Msil_0208; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_0_5; -.
DR   OrthoDB; 1462689at2; -.
DR   Proteomes; UP000002257; 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..399
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411066"
FT   DOMAIN          4..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   399 AA;  43944 MW;  634B82BDAE040F64 CRC64;
     MSLITTTEAL AEVCQRLASH AFVTVDTEFL RETTFWPKLC VVQLASADEA VAVDALASGL
     DLAPLFELMA DPAVVKVFHA ARQDLEIVWN LAKIIPAPLF DTQVAAMVCG FGDQVSYGDL
     VQTVCKVSLD KSSRFTDWSR RPLLPAQVDY AIADVTYLRD IYAILQDKLK ETGRLGWLSD
     EMALLTSPAT YEQHPDNAWE RFRNRVRKPR DLGVLMEVAG WREAEAQARD VPRSRILKDD
     VLIELALAAP RSADALGNLR AFPRGMERSR AGAEILAAIE RGLARDPKTL PKLERDRRTG
     GNGATVELLK VLLRQISESH GVAAKMIANV EDLEAIAADD NAKVAALTGW RRELFGVKAL
     ELKHGRLALT VERGRVVMLE WQEASQEAEE PAAPETAAG