ID J7Q7X3_ECOLX Unreviewed; 375 AA.
AC J7Q7X3; A0A2A2XRG0;
DT 31-OCT-2012, integrated into UniProtKB/TrEMBL.
DT 31-OCT-2012, sequence version 1.
DT 27-MAR-2024, entry version 71.
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=A9X72_10880 {ECO:0000313|EMBL:AVU65708.1}, CR538_11290
GN {ECO:0000313|EMBL:AUK00941.1}, DS732_14770
GN {ECO:0000313|EMBL:AXO07533.1};
OS Escherichia coli.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=562 {ECO:0000313|EMBL:AXO07533.1, ECO:0000313|Proteomes:UP000256244};
RN [1] {ECO:0000313|EMBL:AVU65708.1, ECO:0000313|Proteomes:UP000325046}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=190 {ECO:0000313|EMBL:AVU65708.1,
RC ECO:0000313|Proteomes:UP000325046};
RA Hoffmann M., Sanchez M., Timme R., Bry L.;
RT "Whole genome sequencing of cultured foodborne pathogen.";
RL Submitted (MAR-2017) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:AUK00941.1, ECO:0000313|Proteomes:UP000234238}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=14EC029 {ECO:0000313|EMBL:AUK00941.1,
RC ECO:0000313|Proteomes:UP000234238};
RA Li B., Wang X.;
RT "mcr-1 positive E.coli isolates in China.";
RL Submitted (OCT-2017) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:AXO07533.1, ECO:0000313|Proteomes:UP000256244}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Cq9 {ECO:0000313|EMBL:AXO07533.1}, and cq9
RC {ECO:0000313|Proteomes:UP000256244};
RA Bai L.;
RT "Complete genome sequencing and genomic characterization of five
RT Escherichia coli strains co-producing MCR-1 and ESBLs from different
RT origins in China.";
RL Submitted (AUG-2018) 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; CP024141; AUK00941.1; -; Genomic_DNA.
DR EMBL; CP020520; AVU65708.1; -; Genomic_DNA.
DR EMBL; CP031546; AXO07533.1; -; Genomic_DNA.
DR Proteomes; UP000234238; Chromosome.
DR Proteomes; UP000256244; Chromosome.
DR Proteomes; UP000325046; 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; 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 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};
KW Hydrolase {ECO:0000256|HAMAP-Rule:MF_01899, ECO:0000313|EMBL:AXO07533.1};
KW Nuclease {ECO:0000256|HAMAP-Rule:MF_01899};
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 375 AA; 42776 MW; 1F96F629827F24BF CRC64;
MNYQMITTDD ALASLCEAVR AFPAIALDTE FVRTRTYYPQ LGLIQLFDGE HLALIDPLGI
TDWSPLKAIL RDPSITKFLH AGSEDLEVFL NVFGELPQPL IDTQILAAFC GRPMSWGFAS
MVEEYSGVTL DKSESRTDWL ARPLTERQCE YAAADVWYLL PITAKLMVET EASGWLPAAL
DECRLMQMRR QEVVAPEDAW RDITNAWQLR TRQLACLQLL ADWRLRKARE RDLAVNFVVR
EEHLWSVARY MPGSLGELDS LGLSGSEIRF HGKTLLALVE KAQTLPEEAL PQPMLNLMDM
PGYRKVFKAI KSLITDVSET HKISAELLAS RRQINQLLNW HWKLKPQNNL PELISGWRGE
LMAEALHNLL QEYPQ
//
