ID W3RCV0_9BRAD Unreviewed; 382 AA.
AC W3RCV0;
DT 19-MAR-2014, integrated into UniProtKB/TrEMBL.
DT 19-MAR-2014, sequence version 1.
DT 24-JAN-2024, entry version 35.
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=X566_19275 {ECO:0000313|EMBL:ETR74931.1};
OS Afipia sp. P52-10.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Nitrobacteraceae; Afipia.
OX NCBI_TaxID=1429916 {ECO:0000313|EMBL:ETR74931.1, ECO:0000313|Proteomes:UP000018975};
RN [1] {ECO:0000313|Proteomes:UP000018975}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=P52-10 {ECO:0000313|Proteomes:UP000018975};
RX PubMed=25874801;
RA Pickering B.S., Tyler S., Smith G., Burton L., Li M., Dallaire A.,
RA Weingartl H.;
RT "Identification of a novel afipia species isolated from an Indian flying
RT fox.";
RL PLoS ONE 10:E0121274-E0121274(2015).
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:ETR74931.1}.
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DR EMBL; AZSJ01000007; ETR74931.1; -; Genomic_DNA.
DR RefSeq; WP_034470387.1; NZ_AZSJ01000007.1.
DR AlphaFoldDB; W3RCV0; -.
DR STRING; 1429916.X566_19275; -.
DR PATRIC; fig|1429916.3.peg.3906; -.
DR eggNOG; COG0349; Bacteria.
DR OrthoDB; 9800549at2; -.
DR Proteomes; UP000018975; 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:UP000018975};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 208..289
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 382 AA; 42869 MW; 081CFDC7CC99FEAA CRC64;
MDLIATTEAL AAACERLAKH PVITVDTEFL RETTYYPLLC VIQMASAEEA VVVDALAEGI
DLKPFFDLMG NERVLKVFHA ARQDIEIIWH RAGMLPHPIF DTQVAAMVLG YGDSIAYDAL
VEKITGHRPD KSHRFTDWSR RPLTKEQIVY AEADVTHLRD VFKALDADLK KRGRSDWVSE
EMEVLTSPRT YDNDPTRAWE RLKTRVRKPK ELGVLMEVAA WREREAQSRD VPRSRVLKDD
AIGDIATHAP TSLEKLAHLR SIPKGFERSK WGADIVAAVE RGLGRDPQTL PKLEKPRSNA
AGSAIVELLK VLLRMTSERH HVAAKVIATI DDLEQIAASD KADVPALHGW RRELFGEAAL
ALKHGQLALA IDKGRVVRVE RN
//
