ID A0A0X1T014_PSEAA Unreviewed; 377 AA.
AC A0A0X1T014;
DT 13-APR-2016, integrated into UniProtKB/TrEMBL.
DT 13-APR-2016, sequence version 1.
DT 27-MAR-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=AWM79_08960 {ECO:0000313|EMBL:AMB85428.1};
OS Pseudomonas agarici.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=46677 {ECO:0000313|EMBL:AMB85428.1, ECO:0000313|Proteomes:UP000063229};
RN [1] {ECO:0000313|EMBL:AMB85428.1, ECO:0000313|Proteomes:UP000063229}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCPPB 2472 {ECO:0000313|EMBL:AMB85428.1,
RC ECO:0000313|Proteomes:UP000063229};
RA McClelland M., Jain A., Saraogi P., Mendelson R., Westerman R.,
RA SanMiguel P., Csonka L.;
RL Submitted (JAN-2016) 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}.
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DR EMBL; CP014135; AMB85428.1; -; Genomic_DNA.
DR RefSeq; WP_060782644.1; NZ_CP014135.1.
DR AlphaFoldDB; A0A0X1T014; -.
DR STRING; 46677.AWM79_08960; -.
DR Proteomes; UP000063229; 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 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; 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|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:UP000063229};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 211..291
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 377 AA; 42973 MW; 9CA631B86E958E7C CRC64;
MAIDIHWIRD NDSLGQYCIE WQRLPFVALD TEFMRVDTFY PIAGLIQIGD GMRVYLIDPL
TIDNWLPLAA LLENPAVVKV VHACSEDLEV LLRLTGSLPV PLFDTQLAAA YLNLGFSMGY
SRLVQEVLGI ELPKGETRSD WLQRPLSETQ VSYAAEDALH LAEVYTRLRP QLPHDKYAWV
LEDGAELVAN LRREVDPYEV YREAKLAWKL SRAQLAVLRE LCAWREREAR VRDLPRNRII
REHSLWPLAK SQPDNLVTLA RIEDMHPRTV RQDGEFLLEL IKQASSVPMD QWPPMVPEPL
PIEAGALVKR LRAIGQAEAE RLNIAPELML RKKTLEALIK SGFPDGPYQL PDSLRGWRRE
LMGQALLDSL AIAGEQP
//
