ID   RNPH_RALPJ              Reviewed;         238 AA.
AC   B2U8D8;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-JUL-2008, sequence version 1.
DT   03-AUG-2022, entry version 85.
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=Rpic_2280;
OS   Ralstonia pickettii (strain 12J).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Ralstonia.
OX   NCBI_TaxID=402626;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=12J;
RA   Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA   Bruce D., Goodwin L., Pitluck S., Meincke L., Brettin T., Detter J.C.,
RA   Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L.,
RA   Kyrpides N., Mikhailova N., Marsh T., Richardson P.;
RT   "Complete sequence of chromosome 1 of Ralstonia pickettii 12J.";
RL   Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases.
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; CP001068; ACD27414.1; -; Genomic_DNA.
DR   RefSeq; WP_004630940.1; NC_010682.1.
DR   AlphaFoldDB; B2U8D8; -.
DR   SMR; B2U8D8; -.
DR   STRING; 402626.Rpic_2280; -.
DR   EnsemblBacteria; ACD27414; ACD27414; Rpic_2280.
DR   GeneID; 61390331; -.
DR   KEGG; rpi:Rpic_2280; -.
DR   eggNOG; COG0689; Bacteria.
DR   HOGENOM; CLU_050858_0_0_4; -.
DR   OMA; KGKGQGW; -.
DR   OrthoDB; 1824064at2; -.
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..238
FT                   /note="Ribonuclease PH"
FT                   /id="PRO_1000129361"
FT   REGION          66..88
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        69..83
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         86
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00564"
FT   BINDING         124..126
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00564"
SQ   SEQUENCE   238 AA;  25485 MW;  6E339449BA98534D CRC64;
     MRPSGRQPDQ LRPVTLTRKF TRHAEGSVLV CFGDTQVLCT ASVLPKVPPH KKGSGEGWVT
     AEYGMLPRST HTRSDREAAR GKQSGRTQEI QRLIGRAMRT VFDLRALGEH TLHLDCDVLQ
     ADGGTRTASI TGAFVAAYDA VSVMREKGQL VGDPVRDFVA AVSVGVVDGV PVLDLDYPED
     SACDTDMNVV MTGSGGFVEV QGTAEGTPFS RAEMDAMLGL ADQGIRTLIS LQKQALGL