RNPH_METC4
ID RNPH_METC4 Reviewed; 237 AA.
AC B7L092;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 10-FEB-2009, sequence version 1.
DT 03-AUG-2022, entry version 66.
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=Mchl_0434;
OS Methylorubrum extorquens (strain CM4 / NCIMB 13688) (Methylobacterium
OS extorquens).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Methylobacteriaceae; Methylorubrum.
OX NCBI_TaxID=440085;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CM4 / NCIMB 13688;
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C.,
RA Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N.,
RA Marx C., Richardson P.;
RT "Complete sequence of chromosome of Methylobacterium chloromethanicum
RT CM4.";
RL Submitted (DEC-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; CP001298; ACK81370.1; -; Genomic_DNA.
DR RefSeq; WP_012605547.1; NC_011757.1.
DR AlphaFoldDB; B7L092; -.
DR SMR; B7L092; -.
DR EnsemblBacteria; ACK81370; ACK81370; Mchl_0434.
DR KEGG; mch:Mchl_0434; -.
DR HOGENOM; CLU_050858_0_0_5; -.
DR OMA; KGKGQGW; -.
DR BioCyc; MEXT440085:MCHL_RS02015-MON; -.
DR Proteomes; UP000002385; 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..237
FT /note="Ribonuclease PH"
FT /id="PRO_1000146779"
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 237 AA; 25682 MW; 269A8A9ACA59354D CRC64;
MRPSKRAADA MRDVTLERAV ARYAEGSCLV TFGNTRVLCT ASLEERGPPW LRGSGKGWVT
AEYAMLPRAT HERTRREVNS GKPSGRTQEI QRLIGRSLRA VTNLPALGER QITVDCDVIQ
ADGGTRTASI TGAWVALHDC FAWMRARSII SVDPLKDHVA AVSCGIYKGQ PVLDLDYAED
SAAETDANFV VTGKGGIVEV QGTAELEPFT DEQFLELLRL AKGGVAGLVE LQRKAIA
