ID A0A0J1HI50_9GAMM Unreviewed; 374 AA.
AC A0A0J1HI50;
DT 14-OCT-2015, integrated into UniProtKB/TrEMBL.
DT 14-OCT-2015, sequence version 1.
DT 27-MAR-2024, entry version 28.
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=ABT57_00535 {ECO:0000313|EMBL:KLV11283.1};
OS Photobacterium ganghwense.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Photobacterium.
OX NCBI_TaxID=320778 {ECO:0000313|EMBL:KLV11283.1, ECO:0000313|Proteomes:UP000035909};
RN [1] {ECO:0000313|EMBL:KLV11283.1, ECO:0000313|Proteomes:UP000035909}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 22954 {ECO:0000313|EMBL:KLV11283.1,
RC ECO:0000313|Proteomes:UP000035909};
RA Machado H., Gram L.;
RT "Photobacterium galathea sp. nov.";
RL Submitted (MAY-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:KLV11283.1}.
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DR EMBL; LDOU01000002; KLV11283.1; -; Genomic_DNA.
DR RefSeq; WP_047883242.1; NZ_PYMI01000003.1.
DR AlphaFoldDB; A0A0J1HI50; -.
DR STRING; 320778.ABT57_00535; -.
DR PATRIC; fig|320778.3.peg.112; -.
DR OrthoDB; 9800549at2; -.
DR Proteomes; UP000035909; 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; 2.
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; IPR048579; RNAseD_HRDC_C.
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 Pfam; PF21293; RNAseD_HRDC_C; 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|HAMAP-Rule:MF_01899};
KW Reference proteome {ECO:0000313|Proteomes:UP000035909};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 210..289
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 374 AA; 43081 MW; DE3A1B92416478B6 CRC64;
MNFEVITSAT RLETVCLQAR NQKAVMLDTE FVRTRTLYPK LGLVQLYDGE TLALIDPLEI
DNLEPLWELL RDQSVTKVLH ACGEDLEVFQ YYAGTMPVPM IDTQVMAAFL GYGVSAGFGT
LVKDFLGVEL DKGEARTNWL ARPLTDRQLD YAAADVYYLK PLFDKLLPLV EAKGWSEALE
QECAAQVLKR MRTVDPDMAY LDVKNAWQLN PRQLAILQKV AKWRILEARK RDLALNFVLK
ELNLWKLARF EIKSKAVMDK EGFDNMEIQR HGNRLISLVN EVERMSPAEY PEKIVRLVDL
PGYKQRVKEI KDVVNAVAEE TGLMSEFLAS KKQINQLISW AWKKQYPQDS LPEMLKSWRK
PLFEERVLPL LKTV
//
