ID M2U8V4_9SPHN Unreviewed; 387 AA.
AC M2U8V4;
DT 01-MAY-2013, integrated into UniProtKB/TrEMBL.
DT 01-MAY-2013, sequence version 1.
DT 24-JAN-2024, entry version 38.
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=C725_0307 {ECO:0000313|EMBL:EMD84377.1};
OS Pacificimonas flava.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingosinicellaceae; Pacificimonas.
OX NCBI_TaxID=1234595 {ECO:0000313|EMBL:EMD84377.1, ECO:0000313|Proteomes:UP000011717};
RN [1] {ECO:0000313|EMBL:EMD84377.1, ECO:0000313|Proteomes:UP000011717}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JLT2015 {ECO:0000313|EMBL:EMD84377.1,
RC ECO:0000313|Proteomes:UP000011717};
RX PubMed=23661488;
RA Tang K., Liu K., Li S., Jiao N.;
RT "Draft Genome Sequence of Strain JLT2015T, Belonging to the Family
RT Sphingomonadaceae of the Alphaproteobacteria.";
RL Genome Announc. 1:E00226-13(2013).
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:EMD84377.1}.
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DR EMBL; AMRV01000001; EMD84377.1; -; Genomic_DNA.
DR RefSeq; WP_008599712.1; NZ_JACHGC010000002.1.
DR AlphaFoldDB; M2U8V4; -.
DR PATRIC; fig|1234595.3.peg.307; -.
DR OrthoDB; 9800549at2; -.
DR Proteomes; UP000011717; 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 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|ARBA:ARBA00022722, ECO:0000256|HAMAP-Rule:MF_01899};
KW Reference proteome {ECO:0000313|Proteomes:UP000011717};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 210..291
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 387 AA; 43191 MW; 27EACD718B9F1789 CRC64;
MAEYQFITDT ASLKDLCQRL ERAPFVTVDT EFMRESTYYP DLCLIQVASP DEAAAVDPKA
DMDLSPLLDL ITRAEVLKVM HAAGQDVEII YNRTGETPWP LFDTQIAAMA LGLGEQVSYA
TLVSHYLGHT LDKGARFTDW GRRPLDQRQL DYAIADVTHL AEIFPKMLEG LKQTGRGDWL
DEDMQRLTDP KNYANEPENA WQRVKFPGRN AEALGRLKAL AAWREREAQA KDLPRGRIVK
DETLADLAGH PPKDQQALSR VRGLSKTWAA NDIGERLMKA LADAEPMPKS EIPDKPRGRP
RLNADSSLVA DLLKLLLKVR AKEADVASRL IGRAEDLERL AAGERSGLPL LEGWRYDVFG
ADALALVEGR RSFAVKDGRM VMTEVGD
//
