ID   RND_PSYIN               Reviewed;         369 AA.
AC   A1SVE6;
DT   27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT   06-FEB-2007, sequence version 1.
DT   25-MAY-2022, entry version 74.
DE   RecName: Full=Ribonuclease D {ECO:0000255|HAMAP-Rule:MF_01899};
DE            Short=RNase D {ECO:0000255|HAMAP-Rule:MF_01899};
DE            EC=3.1.13.5 {ECO:0000255|HAMAP-Rule:MF_01899};
GN   Name=rnd {ECO:0000255|HAMAP-Rule:MF_01899}; OrderedLocusNames=Ping_1668;
OS   Psychromonas ingrahamii (strain 37).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Psychromonadaceae; Psychromonas.
OX   NCBI_TaxID=357804;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=37;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Thompson L.S., Brettin T., Bruce D., Han C., Tapia R., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Staley J.,
RA   Richardson P.;
RT   "Complete sequence of Psychromonas ingrahamii 37.";
RL   Submitted (JAN-2007) 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:0000255|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:0000255|HAMAP-Rule:MF_01899};
CC   -!- COFACTOR:
CC       Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01899};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01899}.
CC   -!- SIMILARITY: Belongs to the RNase D family. {ECO:0000255|HAMAP-
CC       Rule:MF_01899}.
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DR   EMBL; CP000510; ABM03461.1; -; Genomic_DNA.
DR   RefSeq; WP_011770021.1; NC_008709.1.
DR   AlphaFoldDB; A1SVE6; -.
DR   SMR; A1SVE6; -.
DR   STRING; 357804.Ping_1668; -.
DR   EnsemblBacteria; ABM03461; ABM03461; Ping_1668.
DR   KEGG; pin:Ping_1668; -.
DR   eggNOG; COG0349; Bacteria.
DR   HOGENOM; CLU_042387_0_1_6; -.
DR   OMA; FMRVDTF; -.
DR   OrthoDB; 1462689at2; -.
DR   Proteomes; UP000000639; 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   Gene3D; 1.10.150.80; -; 2.
DR   Gene3D; 3.30.420.10; -; 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   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; SSF47819; 2.
DR   SUPFAM; SSF53098; SSF53098; 1.
DR   TIGRFAMs; TIGR01388; rnd; 1.
DR   PROSITE; PS50967; HRDC; 1.
PE   3: Inferred from homology;
KW   Cytoplasm; Exonuclease; Hydrolase; Nuclease; Reference proteome;
KW   tRNA processing.
FT   CHAIN           1..369
FT                   /note="Ribonuclease D"
FT                   /id="PRO_0000411070"
FT   DOMAIN          4..168
FT                   /note="3'-5' exonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT   DOMAIN          207..286
FT                   /note="HRDC"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ   SEQUENCE   369 AA;  42462 MW;  031B04F299DD9C58 CRC64;
     MQFEIITTTA QLHDFIATLD GSPISLDTEF VRTRTYAANL GLLQISQNTQ ITLIDPIAVG
     DLSSFWQAID NKNIILHASS EDLEIIRDHK GDLNFTLFDT QIACSFLNMG ASLGYAKMVE
     TLEAVIVDKG ESRTDWCARP LSEKQINYAG VDVLYLQPCL EKLQQQLENK KMFPFFEQEC
     QSVLAQKMVK QDPDKAYKLL NNLFKLDRQG LAIIKALAKW RLLTAQERNL ALNFVVKADH
     LWLLAYYQPT SLDDLRRLNL LPNEIRIHGQ QILTIMTQVI SQDESTYPPL VNRLVDFPAY
     KSTVKSMRDK IQLCAEKYDL PLELLASKRV INEYLSWLWK LTNLQRQTAN KPKLLTGWRF
     ELIGHQFEH