ID A0A0S9CHB5_9SPHN Unreviewed; 391 AA.
AC A0A0S9CHB5;
DT 17-FEB-2016, integrated into UniProtKB/TrEMBL.
DT 17-FEB-2016, sequence version 1.
DT 24-JAN-2024, entry version 27.
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=ASE95_10580 {ECO:0000313|EMBL:KQN93020.1};
OS Sphingomonas sp. Leaf231.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingomonas.
OX NCBI_TaxID=1736301 {ECO:0000313|EMBL:KQN93020.1, ECO:0000313|Proteomes:UP000051427};
RN [1] {ECO:0000313|EMBL:KQN93020.1, ECO:0000313|Proteomes:UP000051427}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Leaf231 {ECO:0000313|EMBL:KQN93020.1,
RC ECO:0000313|Proteomes:UP000051427};
RA Gilbert D.G.;
RL Submitted (OCT-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:KQN93020.1, ECO:0000313|Proteomes:UP000051427}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Leaf231 {ECO:0000313|EMBL:KQN93020.1,
RC ECO:0000313|Proteomes:UP000051427};
RA Schulze-Lefert P.;
RT "Functional overlap of the Arabidopsis leaf and root microbiotas.";
RL Submitted (NOV-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:KQN93020.1}.
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DR EMBL; LMLS01000002; KQN93020.1; -; Genomic_DNA.
DR RefSeq; WP_056635374.1; NZ_LMLS01000002.1.
DR AlphaFoldDB; A0A0S9CHB5; -.
DR STRING; 1736301.ASE95_10580; -.
DR OrthoDB; 9800549at2; -.
DR Proteomes; UP000051427; 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:UP000051427};
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 391 AA; 43079 MW; CD178B515FF74222 CRC64;
MHVHPLITDS ATLANLCARL SDAPFITVDT EFMRESTYYP ELCLIQIADT EEAAAIDPMA
PGIDLTPLLN LLVDNEDVLK VVHAGGQDIE IIYNLTGRTP HPLFDTQVAA MALGQGEQIG
YSNLVDSWLG IQVDKGARFT DWARRPLDAR QIEYAIGDVT HLSNIFPKML DRLKKTGRGA
WLDQEMERLA DPANYANDPD VAWKRVRVSS RKADVLGRLK AIARWRELEA QAKDLPRGRI
VKDETIADLA GHPPRKQADL AKVRGLSQTW AGNDIGARLL AAIDNAAPLS DAEMPPREDR
KPGLGKEGAL VADLLKLLLK IRARDIDVAP RLLARGDELE ALAAGQRDGL QILQGWRFDQ
FGQDALDLVE GRLGFAVQDG RLKMTRTEAA A
//
