ID A0A0Q2YVX2_9RHOB Unreviewed; 385 AA.
AC A0A0Q2YVX2;
DT 20-JAN-2016, integrated into UniProtKB/TrEMBL.
DT 20-JAN-2016, sequence version 1.
DT 24-JAN-2024, entry version 25.
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=AN189_16415 {ECO:0000313|EMBL:KQI67188.1};
OS Loktanella sp. 3ANDIMAR09.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC Roseobacteraceae; Loktanella.
OX NCBI_TaxID=1225657 {ECO:0000313|EMBL:KQI67188.1, ECO:0000313|Proteomes:UP000051463};
RN [1] {ECO:0000313|EMBL:KQI67188.1, ECO:0000313|Proteomes:UP000051463}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=3ANDIMAR09 {ECO:0000313|EMBL:KQI67188.1,
RC ECO:0000313|Proteomes:UP000051463};
RA Mas-Llado M., Nogales B., Bosch R.;
RT "Draft genome sequence of Loktanella sp. 3ANDIMAR09.";
RL Submitted (SEP-2015) 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:KQI67188.1}.
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DR EMBL; LJAK01000015; KQI67188.1; -; Genomic_DNA.
DR RefSeq; WP_056038446.1; NZ_LJAK01000015.1.
DR AlphaFoldDB; A0A0Q2YVX2; -.
DR STRING; 1225657.AN189_16415; -.
DR PATRIC; fig|1225657.3.peg.3372; -.
DR OrthoDB; 9800549at2; -.
DR Proteomes; UP000051463; 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 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|ARBA:ARBA00022839, ECO:0000256|HAMAP-
KW Rule:MF_01899}; Hydrolase {ECO:0000256|HAMAP-Rule:MF_01899};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722, ECO:0000256|HAMAP-Rule:MF_01899};
KW Reference proteome {ECO:0000313|Proteomes:UP000051463};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 212..293
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 385 AA; 43018 MW; 7D3F1EC9231716BE CRC64;
MQTITTTTEL ATFCAEAAKR PYVTVDTEFL RERTYYSKLC LVQLAYRDAA GEDAVLVDPL
VDGLSLEPLY DLFRDPGVVK VFHAARQDLE IFWVDAQLIP APLFDTQVAA MVCGYGDQAG
YETLVRKISK AQLDKSSRFT DWSRRPLTDA QKTYALGDVT YLREIYEVLS DRLRSTGREK
WVQEEMAVLN DPATYQTNPD DAWQRVKTRT TSGRFLAIVR ELARFREEYA QTRDIPRNRV
FKDDVLVELA STKPTDEKDL SRSRLLQREA RKGDIAAGIL AAVKAGLALS NDRLPKPPAG
TERLQVNPAI ADMLRVLLKA KSEQADVAQK LIANAADLDA LAAGQRDLPA LRGWRKEVFG
RDAILLTEGK VALAVDGAQV VTVPR
//
