ID T0I0P6_9SPHN Unreviewed; 228 AA.
AC T0I0P6;
DT 16-OCT-2013, integrated into UniProtKB/TrEMBL.
DT 16-OCT-2013, sequence version 1.
DT 27-MAR-2024, entry version 45.
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 ORFNames=L284_03240 {ECO:0000313|EMBL:EQB18887.1};
OS Novosphingobium lindaniclasticum LE124.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Novosphingobium.
OX NCBI_TaxID=1096930 {ECO:0000313|EMBL:EQB18887.1, ECO:0000313|Proteomes:UP000015527};
RN [1] {ECO:0000313|EMBL:EQB18887.1, ECO:0000313|Proteomes:UP000015527}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LE124 {ECO:0000313|EMBL:EQB18887.1,
RC ECO:0000313|Proteomes:UP000015527};
RX PubMed=24029761;
RA Saxena A., Nayyar N., Sangwan N., Kumari R., Khurana J.P., Lal R.;
RT "Genome Sequence of Novosphingobium lindaniclasticum LE124T, Isolated from
RT a Hexachlorocyclohexane Dumpsite.";
RL Genome Announc. 1:e00715-13(2013).
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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EQB18887.1}.
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DR EMBL; ATHL01000028; EQB18887.1; -; Genomic_DNA.
DR AlphaFoldDB; T0I0P6; -.
DR PATRIC; fig|1096930.3.peg.640; -.
DR eggNOG; COG0689; Bacteria.
DR Proteomes; UP000015527; Unassembled WGS sequence.
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 CDD; cd11362; RNase_PH_bact; 1.
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 InterPro; IPR018336; RNase_PH_CS.
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.
DR PROSITE; PS01277; RIBONUCLEASE_PH; 1.
PE 3: Inferred from homology;
KW Nucleotidyltransferase {ECO:0000256|HAMAP-Rule:MF_00564};
KW Reference proteome {ECO:0000313|Proteomes:UP000015527};
KW RNA-binding {ECO:0000256|ARBA:ARBA00022884};
KW rRNA processing {ECO:0000256|ARBA:ARBA00022552, ECO:0000256|HAMAP-
KW Rule:MF_00564}; Transferase {ECO:0000256|HAMAP-Rule:MF_00564};
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 1..130
FT /note="Exoribonuclease phosphorolytic"
FT /evidence="ECO:0000259|Pfam:PF01138"
FT DOMAIN 148..212
FT /note="Exoribonuclease phosphorolytic"
FT /evidence="ECO:0000259|Pfam:PF03725"
FT BINDING 76
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00564"
FT BINDING 114..116
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00564"
SQ SEQUENCE 228 AA; 24344 MW; 2739E89E04901262 CRC64;
MRAIDIQTGF TKHAEGSVLI SFGDTRVLVT ASVEEKVPPF LRGKGEGWVT AEYSMLPRAT
HTRGSREAAK GKQSGRTQEI QRLIGRSLRA VVDMKKLGER QIVLDCDVLQ ADGGTRTASI
SGAWVALRLA VDKLMAEGKI KEDPITGRVA AISCGICQGT PVLDLDYIED SAADADANFV
LIEGGKIAEA QATAEGATYD EEGLLRLLRL ARIGCDSIFA AQAKAVGR
//