ID C6XKM8_HIRBI Unreviewed; 390 AA.
AC C6XKM8;
DT 22-SEP-2009, integrated into UniProtKB/TrEMBL.
DT 22-SEP-2009, sequence version 1.
DT 24-JAN-2024, entry version 69.
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 OrderedLocusNames=Hbal_1910 {ECO:0000313|EMBL:ACT59595.1};
OS Hirschia baltica (strain ATCC 49814 / DSM 5838 / IFAM 1418).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomonadales;
OC Hyphomonadaceae; Hirschia.
OX NCBI_TaxID=582402 {ECO:0000313|EMBL:ACT59595.1, ECO:0000313|Proteomes:UP000002745};
RN [1] {ECO:0000313|Proteomes:UP000002745}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49814 / DSM 5838 / IFAM 1418
RC {ECO:0000313|Proteomes:UP000002745};
RX PubMed=21705585; DOI=10.1128/JB.05453-11;
RG US DOE Joint Genome Institute;
RA Brown P.J., Kysela D.T., Buechlein A., Hemmerich C., Brun Y.V.;
RT "Genome sequences of eight morphologically diverse alphaproteobacteria.";
RL J. Bacteriol. 193:4567-4568(2011).
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; CP001678; ACT59595.1; -; Genomic_DNA.
DR RefSeq; WP_015827745.1; NC_012982.1.
DR AlphaFoldDB; C6XKM8; -.
DR STRING; 582402.Hbal_1910; -.
DR KEGG; hba:Hbal_1910; -.
DR eggNOG; COG0349; Bacteria.
DR HOGENOM; CLU_042387_0_0_5; -.
DR OMA; FMRVDTF; -.
DR OrthoDB; 9800549at2; -.
DR Proteomes; UP000002745; 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; 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};
KW Hydrolase {ECO:0000256|HAMAP-Rule:MF_01899, ECO:0000313|EMBL:ACT59595.1};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722, ECO:0000256|HAMAP-Rule:MF_01899};
KW Reference proteome {ECO:0000313|Proteomes:UP000002745};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 216..297
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 390 AA; 43834 MW; F86B76F3A01BCE49 CRC64;
MPSNTRDELK LVADTDELIK ACEELKKGEF IAVDTEFHRE STFWPKLCLI QAATLEFDCL
IDPLSPNIDL APFLDLMADT SRVKVFHAAR QDMEIFTKLI GTPPAPIFDS QVAAMACGLG
DSVSYENLVS QLLKARVDKS SQFTDWQRRP LTEKQLDYAR GDVTHLRHCY VKLKAKLEKL
GRMGWIEEET EILVNPDTYD TNPKNAWKRM KIRKPRKDYL ALIASVSEWR EKLAQELDKP
RSRILKDDAV QEIAQQKPID VNAMERLRAV PKGFAKSKHG QTLLEAINAA IADPDAYAPE
IPKRPTNTQP PGAVGDLLKV LLKHVSEEAD VAPRLIANAA DIERIACDVE PDVQAMRGWR
REVFGNLAIK LKQGKIAIAI SDTGVKVFDV
//