RNPH_XYLFT
ID RNPH_XYLFT Reviewed; 241 AA.
AC Q87DG3;
DT 16-JUN-2003, integrated into UniProtKB/Swiss-Prot.
DT 16-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 88.
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=PD_0722;
OS Xylella fastidiosa (strain Temecula1 / ATCC 700964).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Xylella.
OX NCBI_TaxID=183190;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Temecula1 / ATCC 700964;
RX PubMed=12533478; DOI=10.1128/jb.185.3.1018-1026.2003;
RA Van Sluys M.A., de Oliveira M.C., Monteiro-Vitorello C.B., Miyaki C.Y.,
RA Furlan L.R., Camargo L.E.A., da Silva A.C.R., Moon D.H., Takita M.A.,
RA Lemos E.G.M., Machado M.A., Ferro M.I.T., da Silva F.R., Goldman M.H.S.,
RA Goldman G.H., Lemos M.V.F., El-Dorry H., Tsai S.M., Carrer H.,
RA Carraro D.M., de Oliveira R.C., Nunes L.R., Siqueira W.J., Coutinho L.L.,
RA Kimura E.T., Ferro E.S., Harakava R., Kuramae E.E., Marino C.L.,
RA Giglioti E., Abreu I.L., Alves L.M.C., do Amaral A.M., Baia G.S.,
RA Blanco S.R., Brito M.S., Cannavan F.S., Celestino A.V., da Cunha A.F.,
RA Fenille R.C., Ferro J.A., Formighieri E.F., Kishi L.T., Leoni S.G.,
RA Oliveira A.R., Rosa V.E. Jr., Sassaki F.T., Sena J.A.D., de Souza A.A.,
RA Truffi D., Tsukumo F., Yanai G.M., Zaros L.G., Civerolo E.L.,
RA Simpson A.J.G., Almeida N.F. Jr., Setubal J.C., Kitajima J.P.;
RT "Comparative analyses of the complete genome sequences of Pierce's disease
RT and citrus variegated chlorosis strains of Xylella fastidiosa.";
RL J. Bacteriol. 185:1018-1026(2003).
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; AE009442; AAO28591.1; -; Genomic_DNA.
DR RefSeq; WP_004083697.1; NC_004556.1.
DR AlphaFoldDB; Q87DG3; -.
DR SMR; Q87DG3; -.
DR EnsemblBacteria; AAO28591; AAO28591; PD_0722.
DR GeneID; 58016269; -.
DR KEGG; xft:PD_0722; -.
DR HOGENOM; CLU_050858_0_0_6; -.
DR OMA; KGKGQGW; -.
DR Proteomes; UP000002516; Chromosome.
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..241
FT /note="Ribonuclease PH"
FT /id="PRO_0000139954"
FT BINDING 89
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00564"
FT BINDING 127..129
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00564"
SQ SEQUENCE 241 AA; 26215 MW; 92C5817ED4ADD77C CRC64;
MNVSRPSGRQ ADALRPVRIE RAFTCHAEGS VLVSFGNTLV VCTASVEAKV PVFLRNKGEG
WITAEYGMLP RSTHTRSERE AARGKQAGRT LEIQRLIGRA LRTCVDRTAL GERTITLDCD
VLQADGGTRT AAITGAYVAL VDAVRCLEQR GQLKKSPLIG AVAAVSVGIY RGMPVLDLDY
PEDSDCDTDM NVVMNDEGGF IELQGTAEQQ AFRRGELDML LALAERGTAM LFDIQREALA
R