RND_NITHX
ID RND_NITHX Reviewed; 382 AA.
AC Q1QLI8;
DT 27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 2.
DT 25-MAY-2022, entry version 78.
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=Nham_2112;
OS Nitrobacter hamburgensis (strain DSM 10229 / NCIMB 13809 / X14).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Nitrobacter.
OX NCBI_TaxID=323097;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 10229 / NCIMB 13809 / X14;
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 Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Ivanova N., Ward B., Arp D., Klotz M., Stein L.,
RA O'Mullan G., Starkenburg S., Sayavedra L., Poret-Peterson A.T.,
RA Gentry M.E., Bruce D., Richardson P.;
RT "Complete sequence of chromosome of Nitrobacter hamburgensis X14.";
RL Submitted (MAR-2006) 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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABE62909.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; CP000319; ABE62909.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_041358930.1; NC_007964.1.
DR AlphaFoldDB; Q1QLI8; -.
DR SMR; Q1QLI8; -.
DR STRING; 323097.Nham_2112; -.
DR PRIDE; Q1QLI8; -.
DR EnsemblBacteria; ABE62909; ABE62909; Nham_2112.
DR KEGG; nha:Nham_2112; -.
DR eggNOG; COG0349; Bacteria.
DR HOGENOM; CLU_042387_0_0_5; -.
DR OrthoDB; 1462689at2; -.
DR Proteomes; UP000001953; 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; -; 1.
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 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..382
FT /note="Ribonuclease D"
FT /id="PRO_0000411067"
FT DOMAIN 4..169
FT /note="3'-5' exonuclease"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT DOMAIN 208..289
FT /note="HRDC"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
SQ SEQUENCE 382 AA; 42821 MW; 1B036C74C57BA10C CRC64;
MDLITTTAEL ASVCARLANY PVVTVDTEFL RETTYYPLLC VVQMASPDEA VVVDALAEGI
DLKPFFDLMS NERVLKVFHA ARQDIEIVWH QAGIIPHPIF DTQVAAMVLG YGDSIAYDAL
VERVNGHRPD KTHRFTDWSR RPLTKDQLEY AVADVTHLRD VFAALDADLK KRGRGDWVSE
EMEVLTSPKT YDFHPERAWE RLKTRVRKPK DLAVMMEVAA WREQEAQSRN IPRSRVLKDD
AVGDIAIHAP ATPERLATLR SLPKGFEKSQ WGADIVAAVQ RGLARDPREL PKIEKPRNNT
NGAATVELLK VLLRMTSERH AVASKVIATV DDLERIAADD AADVGALRGW RRELFGEAAL
ALKHGQLALA IEKGRVVRVE RS