ID   RNPH_PARPJ              Reviewed;         246 AA.
AC   B2T6B5;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-JUL-2008, sequence version 1.
DT   03-AUG-2022, entry version 64.
DE   RecName: Full=Ribonuclease PH {ECO:0000255|HAMAP-Rule:MF_00564};
DE            Short=RNase PH {ECO:0000255|HAMAP-Rule:MF_00564};
DE            EC=2.7.7.56 {ECO:0000255|HAMAP-Rule:MF_00564};
DE   AltName: Full=tRNA nucleotidyltransferase {ECO:0000255|HAMAP-Rule:MF_00564};
GN   Name=rph {ECO:0000255|HAMAP-Rule:MF_00564}; OrderedLocusNames=Bphyt_3087;
OS   Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN)
OS   (Burkholderia phytofirmans).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Paraburkholderia.
OX   NCBI_TaxID=398527;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 17436 / LMG 22146 / PsJN;
RX   PubMed=21551308; DOI=10.1128/jb.05055-11;
RA   Weilharter A., Mitter B., Shin M.V., Chain P.S., Nowak J., Sessitsch A.;
RT   "Complete genome sequence of the plant growth-promoting endophyte
RT   Burkholderia phytofirmans strain PsJN.";
RL   J. Bacteriol. 193:3383-3384(2011).
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:0000255|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:0000255|HAMAP-Rule:MF_00564};
CC   -!- SUBUNIT: Homohexameric ring arranged as a trimer of dimers.
CC       {ECO:0000255|HAMAP-Rule:MF_00564}.
CC   -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000255|HAMAP-
CC       Rule:MF_00564}.
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DR   EMBL; CP001052; ACD17479.1; -; Genomic_DNA.
DR   RefSeq; WP_012434054.1; NC_010681.1.
DR   AlphaFoldDB; B2T6B5; -.
DR   SMR; B2T6B5; -.
DR   STRING; 398527.Bphyt_3087; -.
DR   EnsemblBacteria; ACD17479; ACD17479; Bphyt_3087.
DR   KEGG; bpy:Bphyt_3087; -.
DR   eggNOG; COG0689; Bacteria.
DR   HOGENOM; CLU_050858_0_0_4; -.
DR   OMA; KGKGQGW; -.
DR   OrthoDB; 1824064at2; -.
DR   Proteomes; UP000001739; Chromosome 1.
DR   GO; GO:0000175; F:3'-5'-exoribonuclease 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   CDD; cd11362; RNase_PH_bact; 1.
DR   Gene3D; 3.30.230.70; -; 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_S5_D2-typ_fold.
DR   InterPro; IPR002381; RNase_PH_bac-type.
DR   InterPro; IPR018336; RNase_PH_CS.
DR   Pfam; PF01138; RNase_PH; 1.
DR   Pfam; PF03725; RNase_PH_C; 1.
DR   SUPFAM; SSF54211; SSF54211; 1.
DR   SUPFAM; SSF55666; SSF55666; 1.
DR   TIGRFAMs; TIGR01966; RNasePH; 1.
DR   PROSITE; PS01277; RIBONUCLEASE_PH; 1.
PE   3: Inferred from homology;
KW   Nucleotidyltransferase; RNA-binding; rRNA processing; Transferase;
KW   tRNA processing; tRNA-binding.
FT   CHAIN           1..246
FT                   /note="Ribonuclease PH"
FT                   /id="PRO_1000129330"
FT   BINDING         91
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00564"
FT   BINDING         129..131
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00564"
SQ   SEQUENCE   246 AA;  26573 MW;  1AF2552E1F25F86E CRC64;
     MTNDTQRPSG RQANQLRDVR ITRHYTKHAE GSVLVEFGDT KVICTASIAE SVPSFLRDRG
     QGWLTAEYGM LPRATHTRSD REAARGKQTG RTQEIQRLIG RALRSVFDLE KLGARTLHID
     CDVIQADGGT RTASITGAFV AAHDAVAKLL ATGRIESSPI TDYVAAISVG VYDGLPVLDL
     DYDEDSQCDT DMNVVMTGAG GFVEIQGTAE GVAFSRDEMN ALLDLASDGI NTLIAKQKAA
     LEQKSE