ID A0A1G5NI95_AFIMA Unreviewed; 396 AA.
AC A0A1G5NI95;
DT 22-NOV-2017, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2017, sequence version 1.
DT 24-JAN-2024, entry version 17.
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=SAMN03080610_02100 {ECO:0000313|EMBL:SCZ37125.1};
OS Afifella marina DSM 2698.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Afifellaceae; Afifella.
OX NCBI_TaxID=1120955 {ECO:0000313|EMBL:SCZ37125.1, ECO:0000313|Proteomes:UP000199347};
RN [1] {ECO:0000313|EMBL:SCZ37125.1, ECO:0000313|Proteomes:UP000199347}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 2698 {ECO:0000313|EMBL:SCZ37125.1,
RC ECO:0000313|Proteomes:UP000199347};
RA de Groot N.N.;
RL Submitted (OCT-2016) 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}.
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DR EMBL; FMVW01000004; SCZ37125.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1G5NI95; -.
DR STRING; 1120955.SAMN03080610_02100; -.
DR OrthoDB; 9800549at2; -.
DR Proteomes; UP000199347; 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:UP000199347};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 214..295
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 396 AA; 44961 MW; 3120D70B6DBA343E CRC64;
MSAKNDYQVI TESEQLAEIC RRFSASPFVS IDTEFIRETT FWARLCLIQM ADPEVAVIVD
PLAEGLDLAP FFELMRNEKV TKVFHAARQD VEIFVKLDGA VPQPLFDTQL AAMVCGYGDQ
ISYDQLVYRV TGVRIDKSSR FTDWQRRPLS QKQLDYAVSD VTHLCDVYRF LKANLEEQKR
SDWVAEELAV LNDVETYRTH PENAWKRLKM RVRKPRQLAV MQKVAAWREK EAQSRDVPRQ
RVLKDEAIYE IALQQPRNAE QMARLRALPR GFERSHSAQA LIAAVEEALA VPDDELPSIP
KPRPAPEHAS ASAELLKVLL KMVSEEHGVA SRLVATVDEL EKIAADDHAD VPAMKGWRRQ
LFGERALALK RGEMALLLGN GRVRAVQVDD MQAAAE
//
