ID   B9KY88_THERP            Unreviewed;       243 AA.
AC   B9KY88;
DT   24-MAR-2009, integrated into UniProtKB/TrEMBL.
DT   24-MAR-2009, sequence version 1.
DT   27-MAR-2024, entry version 80.
DE   RecName: Full=Ribonuclease PH {ECO:0000256|HAMAP-Rule:MF_00564};
DE            Short=RNase PH {ECO:0000256|HAMAP-Rule:MF_00564};
DE            EC=2.7.7.56 {ECO:0000256|HAMAP-Rule:MF_00564};
DE   AltName: Full=tRNA nucleotidyltransferase {ECO:0000256|HAMAP-Rule:MF_00564};
GN   Name=rph {ECO:0000256|HAMAP-Rule:MF_00564,
GN   ECO:0000313|EMBL:ACM05361.1};
GN   OrderedLocusNames=trd_0433 {ECO:0000313|EMBL:ACM05361.1};
OS   Thermomicrobium roseum (strain ATCC 27502 / DSM 5159 / P-2).
OC   Bacteria; Thermomicrobiota; Thermomicrobia; Thermomicrobiales;
OC   Thermomicrobiaceae; Thermomicrobium.
OX   NCBI_TaxID=309801 {ECO:0000313|EMBL:ACM05361.1, ECO:0000313|Proteomes:UP000000447};
RN   [1] {ECO:0000313|EMBL:ACM05361.1, ECO:0000313|Proteomes:UP000000447}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 27502 / DSM 5159 / P-2
RC   {ECO:0000313|Proteomes:UP000000447};
RX   PubMed=19148287; DOI=10.1371/journal.pone.0004207;
RA   Wu D., Raymond J., Wu M., Chatterji S., Ren Q., Graham J.E., Bryant D.A.,
RA   Robb F., Colman A., Tallon L.J., Badger J.H., Madupu R., Ward N.L.,
RA   Eisen J.A.;
RT   "Complete genome sequence of the aerobic CO-oxidizing thermophile
RT   Thermomicrobium roseum.";
RL   PLoS ONE 4:E4207-E4207(2009).
CC   -!- FUNCTION: Phosphorolytic 3'-5' exoribonuclease that plays an important
CC       role in tRNA 3'-end maturation. Removes nucleotide residues following
CC       the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of
CC       RNA molecules by using nucleoside diphosphates as substrates, but this
CC       may not be physiologically important. Probably plays a role in
CC       initiation of 16S rRNA degradation (leading to ribosome degradation)
CC       during starvation. {ECO:0000256|HAMAP-Rule:MF_00564}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate +
CC         tRNA(n); Xref=Rhea:RHEA:10628, Rhea:RHEA-COMP:17343, Rhea:RHEA-
CC         COMP:17344, ChEBI:CHEBI:43474, ChEBI:CHEBI:57930, ChEBI:CHEBI:173114;
CC         EC=2.7.7.56; Evidence={ECO:0000256|HAMAP-Rule:MF_00564};
CC   -!- SUBUNIT: Homohexameric ring arranged as a trimer of dimers.
CC       {ECO:0000256|HAMAP-Rule:MF_00564}.
CC   -!- SIMILARITY: Belongs to the RNase PH family.
CC       {ECO:0000256|ARBA:ARBA00006678, ECO:0000256|HAMAP-Rule:MF_00564}.
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DR   EMBL; CP001275; ACM05361.1; -; Genomic_DNA.
DR   RefSeq; WP_012641838.1; NC_011959.1.
DR   AlphaFoldDB; B9KY88; -.
DR   STRING; 309801.trd_0433; -.
DR   KEGG; tro:trd_0433; -.
DR   eggNOG; COG0689; Bacteria.
DR   HOGENOM; CLU_050858_0_0_0; -.
DR   OrthoDB; 9807456at2; -.
DR   Proteomes; UP000000447; Chromosome.
DR   GO; GO:0000175; F:3'-5'-RNA exonuclease activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0009022; F:tRNA nucleotidyltransferase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0016075; P:rRNA catabolic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR   GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-UniRule.
DR   Gene3D; 3.30.230.70; GHMP Kinase, N-terminal domain; 1.
DR   HAMAP; MF_00564; RNase_PH; 1.
DR   InterPro; IPR001247; ExoRNase_PH_dom1.
DR   InterPro; IPR015847; ExoRNase_PH_dom2.
DR   InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR   InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR   InterPro; IPR020568; Ribosomal_Su5_D2-typ_SF.
DR   InterPro; IPR002381; RNase_PH_bac-type.
DR   NCBIfam; TIGR01966; RNasePH; 1.
DR   PANTHER; PTHR11953; EXOSOME COMPLEX COMPONENT; 1.
DR   PANTHER; PTHR11953:SF2; EXOSOME COMPLEX COMPONENT MTR3; 1.
DR   Pfam; PF01138; RNase_PH; 1.
DR   Pfam; PF03725; RNase_PH_C; 1.
DR   SUPFAM; SSF55666; Ribonuclease PH domain 2-like; 1.
DR   SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 1.
PE   3: Inferred from homology;
KW   Nucleotidyltransferase {ECO:0000256|HAMAP-Rule:MF_00564,
KW   ECO:0000313|EMBL:ACM05361.1};
KW   RNA-binding {ECO:0000256|ARBA:ARBA00022555, ECO:0000256|HAMAP-
KW   Rule:MF_00564};
KW   rRNA processing {ECO:0000256|ARBA:ARBA00022552, ECO:0000256|HAMAP-
KW   Rule:MF_00564};
KW   Transferase {ECO:0000256|HAMAP-Rule:MF_00564, ECO:0000313|EMBL:ACM05361.1};
KW   tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW   Rule:MF_00564};
KW   tRNA-binding {ECO:0000256|ARBA:ARBA00022555, ECO:0000256|HAMAP-
KW   Rule:MF_00564}.
FT   DOMAIN          16..144
FT                   /note="Exoribonuclease phosphorolytic"
FT                   /evidence="ECO:0000259|Pfam:PF01138"
FT   DOMAIN          163..227
FT                   /note="Exoribonuclease phosphorolytic"
FT                   /evidence="ECO:0000259|Pfam:PF03725"
FT   BINDING         90
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00564"
FT   BINDING         128..130
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00564"
SQ   SEQUENCE   243 AA;  26359 MW;  3767B4EE54D2A2C3 CRC64;
     MNELAIPVRH GRANDELRPV EIVPHYIPYA EGSALIMLGN THVLCAATVE ERVPSFLVGS
     GQGWITAEYG MLPRSGRERI PRERMGPGGR TAEIQRLIGR SLRAAVDLAA LGERTIIIDC
     DVLRADGGTR TAAITGGWVA LHLALQHLLA EGRIESLPVV RQVAAVSVGV VAGQPRLDLE
     YAEDSCAEVD MNIVMTDRGE FVELQGTAEG QPFGREVLEQ LLRLAERGIS ELMLVQRRAL
     GLS
//