ID B6VL44_PHOAA Unreviewed; 375 AA.
AC B6VL44; C7BM98;
DT 16-DEC-2008, integrated into UniProtKB/TrEMBL.
DT 16-DEC-2008, sequence version 1.
DT 27-MAR-2024, entry version 85.
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 ECO:0000313|EMBL:CAR66874.1};
GN OrderedLocusNames=PAU_02432 {ECO:0000313|EMBL:CAQ84524.1};
GN ORFNames=PA-RVA6-3045 {ECO:0000313|EMBL:CAR66874.1};
OS Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)
OS (Xenorhabdus luminescens (strain 2)).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Morganellaceae; Photorhabdus.
OX NCBI_TaxID=553480 {ECO:0000313|EMBL:CAR66874.1};
RN [1] {ECO:0000313|EMBL:CAR66874.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=ATCC 43949 {ECO:0000313|EMBL:CAR66874.1};
RX PubMed=18838673; DOI=10.1073/pnas.0711114105;
RA Waterfield N.R., Sanchez-Contreras M., Eleftherianos I., Dowling A.,
RA Wilkinson P., Parkhill J., Thomson N., Reynolds S.E., Bode H.B., Dorus S.,
RA Ffrench-Constant R.H.;
RT "Rapid virulence annotation (RVA): identification of virulence factors
RT using a bacterial genome library and multiple invertebrate hosts.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:15967-15972(2008).
RN [2] {ECO:0000313|EMBL:CAQ84524.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=ATCC43949 {ECO:0000313|EMBL:CAQ84524.1};
RA Crossman L.C.;
RL Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:CAR66874.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=ATCC 43949 {ECO:0000313|EMBL:CAR66874.1};
RA Thomson N.R.;
RL Submitted (SEP-2008) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000313|EMBL:CAQ84524.1, ECO:0000313|Proteomes:UP000002747}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43949 / 3105-77 {ECO:0000313|Proteomes:UP000002747}, and
RC ATCC43949 {ECO:0000313|EMBL:CAQ84524.1};
RX PubMed=19583835; DOI=10.1186/1471-2164-10-302;
RA Wilkinson P., Waterfield N.R., Crossman L., Corton C.,
RA Sanchez-Contreras M., Vlisidou I., Barron A., Bignell A., Clark L.,
RA Ormond D., Mayho M., Bason N., Smith F., Simmonds M., Churcher C.,
RA Harris D., Thompson N.R., Quail M., Parkhill J., ffrench-Constant R.H.;
RT "Comparative genomics of the emerging human pathogen Photorhabdus
RT asymbiotica with the insect pathogen Photorhabdus luminescens.";
RL BMC Genomics 10:302-302(2009).
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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; FM162591; CAQ84524.1; -; Genomic_DNA.
DR EMBL; FM211048; CAR66874.1; -; Genomic_DNA.
DR AlphaFoldDB; B6VL44; -.
DR STRING; 291112.PAU_02432; -.
DR KEGG; pay:PAU_02432; -.
DR eggNOG; COG0349; Bacteria.
DR Proteomes; UP000002747; 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}; Hydrolase {ECO:0000256|HAMAP-Rule:MF_01899};
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; 42528 MW; 71D9327E35CB7579 CRC64;
MNYQLITTDA QLQQVCERAK EYAKIALDTE FVRTRTYYPQ LGLIQLYDGE QLSLIDPLNI
TNWQPFRELI TNPQILKFLH AGSEDLEVFL NAFQCLPEPM IDTQVLAAFI GHPLSCGFAA
LVAEYIHVEL DKSESRTDWL ARPLSEKQCE YAAADVYYLL PLADILITAT TQAGYMEAAI
GECELISQRR REILAPECAY KQIGNICQLR PQQLACLKML AAWRLNQARE RNLAVNFVIR
EENLWQVARY MPTSLAELDA LGLSGQEIRC HGRRLLAMVA ESENIPESEC PPPVTNLIDQ
PGYRKAFKDI KALISQVSEQ HKFNSELLAS RRQINQLLSA HWKLKQLNGK PELLSGWRGG
LLAEPVAEIL ANYPN
//
