ID D4E5K6_SEROD Unreviewed; 373 AA.
AC D4E5K6;
DT 18-MAY-2010, integrated into UniProtKB/TrEMBL.
DT 18-MAY-2010, sequence version 1.
DT 27-MAR-2024, entry version 55.
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 ECO:0000313|EMBL:EFE95022.1};
GN ORFNames=HMPREF0758_3456 {ECO:0000313|EMBL:EFE95022.1};
OS Serratia odorifera DSM 4582.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Serratia.
OX NCBI_TaxID=667129 {ECO:0000313|EMBL:EFE95022.1, ECO:0000313|Proteomes:UP000005723};
RN [1] {ECO:0000313|EMBL:EFE95022.1, ECO:0000313|Proteomes:UP000005723}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 4582 {ECO:0000313|EMBL:EFE95022.1,
RC ECO:0000313|Proteomes:UP000005723};
RA Muzny D., Qin X., Deng J., Jiang H., Liu Y., Qu J., Song X.-Z., Zhang L.,
RA Thornton R., Coyle M., Francisco L., Jackson L., Javaid M., Korchina V.,
RA Kovar C., Mata R., Mathew T., Ngo R., Nguyen L., Nguyen N., Okwuonu G.,
RA Ongeri F., Pham C., Simmons D., Wilczek-Boney K., Hale W., Jakkamsetti A.,
RA Pham P., Ruth R., San Lucas F., Warren J., Zhang J., Zhao Z., Zhou C.,
RA Zhu D., Lee S., Bess C., Blankenburg K., Forbes L., Fu Q., Gubbala S.,
RA Hirani K., Jayaseelan J.C., Lara F., Munidasa M., Palculict T., Patil S.,
RA Pu L.-L., Saada N., Tang L., Weissenberger G., Zhu Y., Hemphill L.,
RA Shang Y., Youmans B., Ayvaz T., Ross M., Santibanez J., Aqrawi P.,
RA Gross S., Joshi V., Fowler G., Nazareth L., Reid J., Worley K.,
RA Petrosino J., Highlander S., Gibbs R.;
RL Submitted (JAN-2010) 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:EFE95022.1}.
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DR EMBL; ADBY01000050; EFE95022.1; -; Genomic_DNA.
DR RefSeq; WP_004962192.1; NZ_GG753567.1.
DR AlphaFoldDB; D4E5K6; -.
DR STRING; 667129.HMPREF0758_3456; -.
DR HOGENOM; CLU_042387_0_1_6; -.
DR OrthoDB; 9800549at2; -.
DR Proteomes; UP000005723; 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; 2.
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; IPR048579; RNAseD_HRDC_C.
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 Pfam; PF21293; RNAseD_HRDC_C; 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};
KW Hydrolase {ECO:0000256|HAMAP-Rule:MF_01899, ECO:0000313|EMBL:EFE95022.1};
KW Nuclease {ECO:0000256|HAMAP-Rule:MF_01899};
KW Reference proteome {ECO:0000313|Proteomes:UP000005723};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01899}.
FT DOMAIN 210..289
FT /note="HRDC"
FT /evidence="ECO:0000259|PROSITE:PS50967"
SQ SEQUENCE 373 AA; 41932 MW; 7B124B7541B5FC93 CRC64;
MNYTLITTDA GLQQVCEQAR KHAQIALDTE FVRTRTYYPQ LGLIQLYDGE QLSLIDPLPI
KQWQPFVDLL ADSAVVKFLH AGSEDLEVFL NAFNTLPTPL VDTQILAAFT GKPLSCGFAT
LVAQYMQVEL DKSESRTDWL ARPLTERQCV YAAADVFYLL PMARQLVQET EQAGWTAAAS
SECLLLCQRR SETLAPELAY REITNAWQLR ARQLGCLQKL AEWRLRQARE RDLAVNFVVR
EENLWAVARH MPGSLGELDA LGLSGPEIRY HGKTLLALVE EANQMDESAL PPPVASLIDQ
PGYKKVFKDI KAAIVTVSEQ SGLSSELLAS RRQINQLLNW HWKLKNGDGL PELISGWRAE
LLAEPLQAIL KNY
//
