ID S2ZNL3_9ACTN Unreviewed; 417 AA.
AC S2ZNL3;
DT 18-SEP-2013, integrated into UniProtKB/TrEMBL.
DT 18-SEP-2013, sequence version 1.
DT 13-SEP-2023, entry version 36.
DE RecName: Full=Ribonuclease D {ECO:0000256|HAMAP-Rule:MF_01899};
DE Short=RNase D {ECO:0000256|HAMAP-Rule:MF_01899};
DE EC=3.1.13.5 {ECO:0000256|HAMAP-Rule:MF_01899};
GN Name=rnd {ECO:0000256|HAMAP-Rule:MF_01899};
GN ORFNames=HMPREF1527_00258 {ECO:0000313|EMBL:EPD77956.1};
OS Atopobium sp. oral taxon 199 str. F0494.
OC Bacteria; Actinomycetota; Coriobacteriia; Coriobacteriales; Atopobiaceae;
OC Atopobium.
OX NCBI_TaxID=1203602 {ECO:0000313|EMBL:EPD77956.1, ECO:0000313|Proteomes:UP000014384};
RN [1] {ECO:0000313|EMBL:EPD77956.1, ECO:0000313|Proteomes:UP000014384}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=F0494 {ECO:0000313|EMBL:EPD77956.1,
RC ECO:0000313|Proteomes:UP000014384};
RG The Broad Institute Genomics Platform;
RA Earl A., Ward D., Feldgarden M., Gevers D., Kirega A., Tanner A.C.,
RA Dewhirst F.D., Izard J., Walker B., Young S., Zeng Q., Gargeya S.,
RA Fitzgerald M., Haas B., Abouelleil A., Allen A.W., Alvarado L.,
RA Arachchi H.M., Berlin A.M., Chapman S.B., Gainer-Dewar J., Goldberg J.,
RA Griggs A., Gujja S., Hansen M., Howarth C., Imamovic A., Ireland A.,
RA Larimer J., McCowan C., Murphy C., Pearson M., Poon T.W., Priest M.,
RA Roberts A., Saif S., Shea T., Sisk P., Sykes S., Wortman J., Nusbaum C.,
RA Birren B.;
RT "The Genome Sequence of Atopobium sp. oral taxon 199 F0494.";
RL Submitted (MAY-2013) 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:0000256|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:0000256|HAMAP-Rule:MF_01899};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01899};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01899}.
CC -!- SIMILARITY: Belongs to the RNase D family. {ECO:0000256|HAMAP-
CC Rule:MF_01899}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EPD77956.1}.
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DR EMBL; ATCH01000001; EPD77956.1; -; Genomic_DNA.
DR AlphaFoldDB; S2ZNL3; -.
DR STRING; 1203602.HMPREF1527_00258; -.
DR PATRIC; fig|1203602.3.peg.266; -.
DR eggNOG; COG0349; Bacteria.
DR HOGENOM; CLU_042387_0_0_11; -.
DR Proteomes; UP000014384; Unassembled WGS sequence.
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 CDD; cd06142; RNaseD_exo; 1.
DR Gene3D; 1.10.150.80; HRDC domain; 1.
DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 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 NCBIfam; TIGR01388; rnd; 1.
DR PANTHER; PTHR47649; RIBONUCLEASE D; 1.
DR PANTHER; PTHR47649:SF1; RIBONUCLEASE D; 1.
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; HRDC-like; 2.
DR SUPFAM; SSF53098; Ribonuclease H-like; 1.
DR PROSITE; PS50967; HRDC; 1.
PE 3: Inferred from homology;
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01899};
KW Exonuclease {ECO:0000256|HAMAP-Rule:MF_01899};
KW Hydrolase {ECO:0000256|HAMAP-Rule:MF_01899};
KW Nuclease {ECO:0000256|HAMAP-Rule:MF_01899};
KW Reference proteome {ECO:0000313|Proteomes:UP000014384};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 248..327
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 417 AA; 46459 MW; DD1DEB89D160AD37 CRC64;
MGIIKSGMSG TSVMSIVSGM SVVFVMSAIS DGSVTVVEWD ALYISTQEEL ASFCARAAHA
RVLAVDTEFL REKTYYPQLC LVQVSTGEEI AAIDPLRINN LSPLKALLED EAIIKVIHAC
SQDLEVLLEG MNCACAPVFD TQLAAAFLGM RQQASYASVV ERYTGVHLAK AESLTDWSRR
PLDPEQLTYA EDDVRYLPDI YRQMYDRLVK TDRLGWLMPE MNDYTVIEHF RRDPREAYLH
LKRSSSLTRR QMAIAREVCA WREALAARRN VPRKWILSDE VLVELCRRVP GTPEKLHKIR
GTESLSQESV SKLLHAIRRG KELPAELCPA IEHHTRPAMG AEGVIDLMYA LVKIVAEKEG
IAPQLIANKG DLADLLAQKE DAKLAGGWRF EVVGKELLGL LAGEVGLTVK NGRVELL
//
