RNPH_AQUAE
ID RNPH_AQUAE Reviewed; 255 AA.
AC O67069;
DT 15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 120.
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}; Synonyms=rnpH;
GN OrderedLocusNames=aq_924;
OS Aquifex aeolicus (strain VF5).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex.
OX NCBI_TaxID=224324;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VF5;
RX PubMed=9537320; DOI=10.1038/32831;
RA Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.,
RA Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R.,
RA Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.;
RT "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.";
RL Nature 392:353-358(1998).
RN [2] {ECO:0007744|PDB:1UDN, ECO:0007744|PDB:1UDO, ECO:0007744|PDB:1UDQ, ECO:0007744|PDB:1UDS}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF WILD-TYPE AND 3 MUTANT PROTEINS
RP WITH SUBSTRATE, SUBUNIT, AND MUTAGENESIS OF ARG-86; THR-125 AND ARG-126.
RX PubMed=12746447; DOI=10.1074/jbc.m300639200;
RA Ishii R., Nureki O., Yokoyama S.;
RT "Crystal structure of the tRNA processing enzyme RNase PH from Aquifex
RT aeolicus.";
RL J. Biol. Chem. 278:32397-32404(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 (PubMed:12746447). {ECO:0000255|HAMAP-Rule:MF_00564,
CC ECO:0000269|PubMed:12746447}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000255|HAMAP-
CC Rule:MF_00564}.
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DR EMBL; AE000657; AAC07032.1; -; Genomic_DNA.
DR PIR; B70380; B70380.
DR RefSeq; NP_213631.1; NC_000918.1.
DR RefSeq; WP_010880569.1; NC_000918.1.
DR PDB; 1UDN; X-ray; 2.30 A; A=1-255.
DR PDB; 1UDO; X-ray; 2.30 A; A=1-255.
DR PDB; 1UDQ; X-ray; 2.30 A; A=1-255.
DR PDB; 1UDS; X-ray; 2.30 A; A=1-255.
DR PDBsum; 1UDN; -.
DR PDBsum; 1UDO; -.
DR PDBsum; 1UDQ; -.
DR PDBsum; 1UDS; -.
DR AlphaFoldDB; O67069; -.
DR SMR; O67069; -.
DR STRING; 224324.aq_924; -.
DR EnsemblBacteria; AAC07032; AAC07032; aq_924.
DR KEGG; aae:aq_924; -.
DR PATRIC; fig|224324.8.peg.724; -.
DR eggNOG; COG0689; Bacteria.
DR HOGENOM; CLU_050858_0_0_0; -.
DR InParanoid; O67069; -.
DR OMA; KGKGQGW; -.
DR OrthoDB; 1824064at2; -.
DR EvolutionaryTrace; O67069; -.
DR Proteomes; UP000000798; 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; IBA:GO_Central.
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 1: Evidence at protein level;
KW 3D-structure; Nucleotidyltransferase; Reference proteome; RNA-binding;
KW rRNA processing; Transferase; tRNA processing; tRNA-binding.
FT CHAIN 1..255
FT /note="Ribonuclease PH"
FT /id="PRO_0000139861"
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,
FT ECO:0000269|PubMed:12746447"
FT MUTAGEN 86
FT /note="R->A: No processing of pre-tRNA-CCA-N(8), binds tRNA
FT as well as wild-type."
FT /evidence="ECO:0000269|PubMed:12746447"
FT MUTAGEN 125
FT /note="T->A: Poor processing of pre-tRNA-CCA-N(8), removes
FT a few nucleotides, binds tRNA better than wild-type."
FT /evidence="ECO:0000269|PubMed:12746447"
FT MUTAGEN 126
FT /note="R->A: Decreased processing of pre-tRNA-CCA-N(8),
FT removes perhaps 4/8 nucleotides, binds tRNA slightly less
FT well than wild-type."
FT /evidence="ECO:0000269|PubMed:12746447"
FT STRAND 14..18
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 21..32
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 35..45
FT /evidence="ECO:0007829|PDB:1UDN"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 58..65
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 67..69
FT /evidence="ECO:0007829|PDB:1UDS"
FT TURN 78..80
FT /evidence="ECO:0007829|PDB:1UDO"
FT HELIX 85..101
FT /evidence="ECO:0007829|PDB:1UDN"
FT HELIX 104..107
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 111..120
FT /evidence="ECO:0007829|PDB:1UDN"
FT HELIX 125..146
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 149..152
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 159..167
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 170..174
FT /evidence="ECO:0007829|PDB:1UDN"
FT HELIX 177..181
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 184..192
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 197..206
FT /evidence="ECO:0007829|PDB:1UDN"
FT HELIX 211..233
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 236..239
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 242..245
FT /evidence="ECO:0007829|PDB:1UDN"
FT STRAND 249..252
FT /evidence="ECO:0007829|PDB:1UDN"
SQ SEQUENCE 255 AA; 28372 MW; 7131CCD8AEDC3917 CRC64;
MRSDGRKEDQ LRPVSIQRDF LEYPEGSCLI SFGKTKVICT ASVIENVPNW LKGKGQGWIT
AEYSMLPRAT QQRTIRESVQ GRIGGRTHEI QRMIGRAMRT AVELTKIGER TIWVDCDVIQ
ADGGTRTAAI TGAFVAVADA IIKLHKEGII EETPIKDFVA AVSVGIVNDR ILLDLNFEED
SAAQVDMNVV GTGSGRLSEV HTMGEEYSFT KDELIKMLDL AQKGINELIE LQKKLYVIQD
GKWERSELKE VSSTT
