RNPH_PSEAE
ID RNPH_PSEAE Reviewed; 239 AA.
AC P50597;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 08-DEC-2000, sequence version 2.
DT 03-AUG-2022, entry version 128.
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=PA5334;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=8824606; DOI=10.1128/jb.178.19.5627-5635.1996;
RA Macgregor C.H., Arora S.K., Hager P.W., Dail M.B., Phibbs P.V. Jr.;
RT "The nucleotide sequence of the Pseudomonas aeruginosa pyrE-crc-rph region
RT and the purification of the crc gene product.";
RL J. Bacteriol. 178:5627-5635(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [3] {ECO:0007744|PDB:1R6L, ECO:0007744|PDB:1R6M}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) WITH AND WITHOUT SUBSTRATE, SUBUNIT,
RP TRNA-BINDING, AND MUTAGENESIS OF 69-ARG--ARG-77; ARG-69; 74-ARG--ARG-77;
RP ARG-74; ARG-77 AND ARG-127.
RX PubMed=14573594; DOI=10.1074/jbc.m309628200;
RA Choi J.M., Park E.Y., Kim J.H., Chang S.K., Cho Y.;
RT "Probing the functional importance of the hexameric ring structure of RNase
RT PH.";
RL J. Biol. Chem. 279:755-764(2004).
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; dimeric
CC protein does not seem to be catalytically active (PubMed:14573594).
CC {ECO:0000255|HAMAP-Rule:MF_00564, ECO:0000305|PubMed:14573594}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000255|HAMAP-
CC Rule:MF_00564}.
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DR EMBL; U38241; AAC44429.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG08719.1; -; Genomic_DNA.
DR PIR; D82978; D82978.
DR RefSeq; NP_254021.1; NC_002516.2.
DR RefSeq; WP_003096595.1; NZ_QZGE01000020.1.
DR PDB; 1R6L; X-ray; 1.90 A; A=1-239.
DR PDB; 1R6M; X-ray; 2.00 A; A=1-239.
DR PDBsum; 1R6L; -.
DR PDBsum; 1R6M; -.
DR AlphaFoldDB; P50597; -.
DR SMR; P50597; -.
DR STRING; 287.DR97_2705; -.
DR DrugBank; DB03309; N-cyclohexyltaurine.
DR PaxDb; P50597; -.
DR PRIDE; P50597; -.
DR DNASU; 878218; -.
DR EnsemblBacteria; AAG08719; AAG08719; PA5334.
DR GeneID; 878218; -.
DR KEGG; pae:PA5334; -.
DR PATRIC; fig|208964.12.peg.5589; -.
DR PseudoCAP; PA5334; -.
DR HOGENOM; CLU_050858_0_0_6; -.
DR InParanoid; P50597; -.
DR OMA; KGKGQGW; -.
DR PhylomeDB; P50597; -.
DR BioCyc; PAER208964:G1FZ6-5456-MON; -.
DR EvolutionaryTrace; P50597; -.
DR Proteomes; UP000002438; 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..239
FT /note="Ribonuclease PH"
FT /id="PRO_0000139924"
FT BINDING 87
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:14573594"
FT BINDING 125..127
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:14573594"
FT MUTAGEN 69..77
FT /note="RSTGERNQR->SSTGERNQS: No longer forms hexamers, no
FT exonuclease activity, does not bind pre-tRNA."
FT /evidence="ECO:0000269|PubMed:14573594"
FT MUTAGEN 69
FT /note="R->S: Still forms hexamers, wild-type exonuclease
FT activity at 30 degrees Celsius, nearly wild-type at 50
FT degrees Celsius, decreased binding of pre-tRNA."
FT /evidence="ECO:0000269|PubMed:14573594"
FT MUTAGEN 74..77
FT /note="RNQR->SNQS: No longer forms hexamers, no exonuclease
FT activity, does not bind pre-tRNA."
FT /evidence="ECO:0000269|PubMed:14573594"
FT MUTAGEN 74
FT /note="R->S: No longer forms hexamers, no exonuclease
FT activity, does not bind pre-tRNA."
FT /evidence="ECO:0000269|PubMed:14573594"
FT MUTAGEN 77
FT /note="R->S: Still forms hexamers, no exonuclease activity,
FT does not bind pre-tRNA."
FT /evidence="ECO:0000269|PubMed:14573594"
FT MUTAGEN 127
FT /note="R->A: Still forms hexamers, wild-type exonuclease
FT activity at 30 degrees Celsius, significantly reduced
FT activity at 50 degrees Celsius, binds pre-tRNA."
FT /evidence="ECO:0000269|PubMed:14573594"
FT CONFLICT 68
FT /note="P -> R (in Ref. 1; AAC44429)"
FT /evidence="ECO:0000305"
FT CONFLICT 96
FT /note="G -> D (in Ref. 1; AAC44429)"
FT /evidence="ECO:0000305"
FT CONFLICT 122
FT /note="A -> T (in Ref. 1; AAC44429)"
FT /evidence="ECO:0000305"
FT CONFLICT 137
FT /note="A -> S (in Ref. 1; AAC44429)"
FT /evidence="ECO:0000305"
FT CONFLICT 149
FT /note="G -> V (in Ref. 1; AAC44429)"
FT /evidence="ECO:0000305"
FT CONFLICT 159
FT /note="M -> I (in Ref. 1; AAC44429)"
FT /evidence="ECO:0000305"
FT CONFLICT 186
FT /note="T -> S (in Ref. 1; AAC44429)"
FT /evidence="ECO:0000305"
FT CONFLICT 195..197
FT /note="AGG -> CRR (in Ref. 1; AAC44429)"
FT /evidence="ECO:0000305"
FT CONFLICT 230..232
FT /note="FEL -> VRT (in Ref. 1; AAC44429)"
FT /evidence="ECO:0000305"
FT STRAND 15..20
FT /evidence="ECO:0007829|PDB:1R6L"
FT STRAND 22..33
FT /evidence="ECO:0007829|PDB:1R6L"
FT STRAND 36..47
FT /evidence="ECO:0007829|PDB:1R6L"
FT STRAND 59..66
FT /evidence="ECO:0007829|PDB:1R6L"
FT STRAND 70..73
FT /evidence="ECO:0007829|PDB:1R6L"
FT HELIX 78..81
FT /evidence="ECO:0007829|PDB:1R6L"
FT HELIX 86..101
FT /evidence="ECO:0007829|PDB:1R6L"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:1R6L"
FT STRAND 110..121
FT /evidence="ECO:0007829|PDB:1R6L"
FT HELIX 126..147
FT /evidence="ECO:0007829|PDB:1R6L"
FT STRAND 160..168
FT /evidence="ECO:0007829|PDB:1R6L"
FT STRAND 171..175
FT /evidence="ECO:0007829|PDB:1R6L"
FT HELIX 178..183
FT /evidence="ECO:0007829|PDB:1R6L"
FT STRAND 185..193
FT /evidence="ECO:0007829|PDB:1R6L"
FT STRAND 198..208
FT /evidence="ECO:0007829|PDB:1R6L"
FT HELIX 212..237
FT /evidence="ECO:0007829|PDB:1R6L"
SQ SEQUENCE 239 AA; 25654 MW; 76F4717C31261EF7 CRC64;
MNRPSGRAAD QLRPIRITRH YTKHAEGSVL VEFGDTKVIC TVSAESGVPR FLKGQGQGWL
TAEYGMLPRS TGERNQREAS RGKQGGRTLE IQRLIGRSLR AALDLSKLGE NTLYIDCDVI
QADGGTRTAS ITGATVALID ALAVLKKRGA LKGNPLKQMV AAVSVGIYQG VPVLDLDYLE
DSAAETDLNV VMTDAGGFIE VQGTAEGAPF RPAELNAMLE LAQQGMQELF ELQRAALAE
