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Database: UniProt
Entry: D3DFP2_HYDTT
LinkDB: D3DFP2_HYDTT
Original site: D3DFP2_HYDTT 
ID   D3DFP2_HYDTT            Unreviewed;       253 AA.
AC   D3DFP2;
DT   23-MAR-2010, integrated into UniProtKB/TrEMBL.
DT   23-MAR-2010, sequence version 1.
DT   24-JAN-2024, entry version 79.
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   ECO:0000313|EMBL:BAI68644.1};
GN   OrderedLocusNames=HTH_0177 {ECO:0000313|EMBL:BAI68644.1};
OS   Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6).
OC   Bacteria; Aquificota; Aquificae; Aquificales; Aquificaceae;
OC   Hydrogenobacter.
OX   NCBI_TaxID=608538 {ECO:0000313|EMBL:BAI68644.1, ECO:0000313|Proteomes:UP000002574};
RN   [1] {ECO:0000313|EMBL:BAI68644.1, ECO:0000313|Proteomes:UP000002574}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 6534 / IAM 12695 / TK-6 [Tokyo]
RC   {ECO:0000313|Proteomes:UP000002574};
RX   PubMed=20348262; DOI=10.1128/JB.00158-10;
RA   Arai H., Kanbe H., Ishii M., Igarashi Y.;
RT   "Complete genome sequence of the thermophilic, obligately
RT   chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter
RT   thermophilus TK-6.";
RL   J. Bacteriol. 192:2651-2652(2010).
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}.
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DR   EMBL; AP011112; BAI68644.1; -; Genomic_DNA.
DR   RefSeq; WP_012962827.1; NC_017161.1.
DR   AlphaFoldDB; D3DFP2; -.
DR   STRING; 608538.HTH_0177; -.
DR   KEGG; hth:HTH_0177; -.
DR   PATRIC; fig|608538.5.peg.178; -.
DR   eggNOG; COG0689; Bacteria.
DR   OMA; RYNMAPF; -.
DR   OrthoDB; 9807456at2; -.
DR   Proteomes; UP000002574; Chromosome.
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:SF0; EXOSOME COMPLEX COMPONENT RRP41; 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:UP000002574};
KW   RNA-binding {ECO:0000256|ARBA:ARBA00022555, ECO:0000256|HAMAP-
KW   Rule:MF_00564};
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          10..142
FT                   /note="Exoribonuclease phosphorolytic"
FT                   /evidence="ECO:0000259|Pfam:PF01138"
FT   DOMAIN          157..223
FT                   /note="Exoribonuclease phosphorolytic"
FT                   /evidence="ECO:0000259|Pfam:PF03725"
FT   BINDING         86
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00564"
FT   BINDING         124..126
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /ligand_note="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00564"
SQ   SEQUENCE   253 AA;  28022 MW;  86D2381DE0256E2B CRC64;
     MRKDGRKPNE LRPIRIVRDY LQHPEGSCLI EFGNTKVICT VSVQDGVPPF LKGKGQGWIT
     AEYSMLPRAT ITRNVRESVQ GRISGRTHEI QRMIGRAMRT ALDLTKIGER TFWIDCDVIQ
     ADGGTRTASI TGAFVAIADA VIKLYNEGIL SSTPIKDFVA SVSVGTVNGQ ILLDLNYEED
     STASVDMNVV ATGSGRISEI QALGEENTFS REEFDRMLSL ALAGISQLIE LQRAFYEIVG
     NVWKRKNVKE ARL
//
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