ID A0A0N1BHP5_9SPHN Unreviewed; 409 AA.
AC A0A0N1BHP5;
DT 09-DEC-2015, integrated into UniProtKB/TrEMBL.
DT 09-DEC-2015, sequence version 1.
DT 24-JAN-2024, entry version 24.
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=IP68_00820 {ECO:0000313|EMBL:KPF77254.1};
OS Blastomonas sp. AAP25.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Blastomonas.
OX NCBI_TaxID=1523416 {ECO:0000313|EMBL:KPF77254.1, ECO:0000313|Proteomes:UP000037930};
RN [1] {ECO:0000313|EMBL:KPF77254.1, ECO:0000313|Proteomes:UP000037930}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AAP25 {ECO:0000313|EMBL:KPF77254.1,
RC ECO:0000313|Proteomes:UP000037930};
RA Zeng Y., Feng F., Liu Y., Koblizek M.;
RT "Novel Diversity of Limnic Aerobic Anoxygenic Phototrophic Bacteria as
RT Revealed by High-throughput Strain Identification and Genome Sequencing.";
RL Submitted (AUG-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:KPF77254.1}.
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DR EMBL; LJHP01000001; KPF77254.1; -; Genomic_DNA.
DR RefSeq; WP_054133236.1; NZ_LJHP01000001.1.
DR AlphaFoldDB; A0A0N1BHP5; -.
DR PATRIC; fig|1523416.3.peg.167; -.
DR OrthoDB; 9800549at2; -.
DR Proteomes; UP000037930; 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:UP000037930};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 212..293
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 409 AA; 45245 MW; CCA1F949C536AB6C CRC64;
MQIHPLITDT DSLARLCTRL AQSDFVAVDT EFMRENTYWP ELCLVQIGNL EEAAAIDPKA
PGIDLSPLLD LLTENPEVLK VFHAGPQDIE IIFNLTGKTP TPLFDTQVAA MALGQAEQIG
YANLVESWLG LTVDKGARFT DWSRRPLEAR QIDYAIGDVT HLAKIFPKML DKLRRTGRGA
WLDIEMEKLG DPRQYKPDPD TLWQRIRPPG RSAQILGRMR ALAWWRETEA QDKNLPRGRI
MKDETLADIA AHPPSHQSDL GKVRGLSAAW RENDIGARMM DALIAARPLS PAEMPPKSPR
GPALGKEGAL VADLLKLLLK IRSREIDVAA RLLARSDDLE ALAAGVRKNL PILEGWRFEQ
FGRDALALVE GRMAFAIADG RIKMTRTELA AEAEPDADAA VAAALAEQP
//
