RNPH_BACSU
ID RNPH_BACSU Reviewed; 245 AA.
AC P28619;
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-1992, sequence version 1.
DT 03-AUG-2022, entry version 138.
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=BSU28370;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1624460; DOI=10.1128/jb.174.14.4727-4735.1992;
RA Craven M.G., Henner D.J., Alessi D., Schauer A.T., Ost K.A.,
RA Deutscher M.P., Friedman D.I.;
RT "Identification of the rph (RNase PH) gene of Bacillus subtilis: evidence
RT for suppression of cold-sensitive mutations in Escherichia coli.";
RL J. Bacteriol. 174:4727-4735(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=8969504; DOI=10.1099/13500872-142-11-3067;
RA Wipat A., Carter N., Brignell C.S., Guy J.B., Piper K., Sanders J.,
RA Emmerson P.T., Harwood C.R.;
RT "The dnaB-pheA (256 degrees-240 degrees) region of the Bacillus subtilis
RT chromosome containing genes responsible for stress responses, the
RT utilization of plant cell walls and primary metabolism.";
RL Microbiology 142:3067-3078(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP FUNCTION IN 23S RRNA PROCESSING, RNASE ACTIVITY, AND DISRUPTION PHENOTYPE.
RX PubMed=19880604; DOI=10.1128/jb.01096-09;
RA Redko Y., Condon C.;
RT "Maturation of 23S rRNA in Bacillus subtilis in the absence of Mini-III.";
RL J. Bacteriol. 192:356-359(2010).
RN [5] {ECO:0007744|PDB:1OYP, ECO:0007744|PDB:1OYR, ECO:0007744|PDB:1OYS}
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, SUBUNIT,
RP AND MUTAGENESIS OF 68-ARG--ARG-76.
RX PubMed=14767080; DOI=10.1110/ps.03477004;
RA Harlow L.S., Kadziola A., Jensen K.F., Larsen S.;
RT "Crystal structure of the phosphorolytic exoribonuclease RNase PH from
RT Bacillus subtilis and implications for its quaternary structure and tRNA
RT binding.";
RL Protein Sci. 13:668-677(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. Plays a role in the secondary pathway of 23S rRNA 3'
CC end maturation (PubMed:19880604). {ECO:0000255|HAMAP-Rule:MF_00564,
CC ECO:0000269|PubMed:19880604}.
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:14767080). It has been suggested that the active form is the
CC dimer which binds tRNA and that the hexameric form protects the
CC substrate recognition loop (approximately residues 65-82) from
CC proteolysis (PubMed:14767080). {ECO:0000255|HAMAP-Rule:MF_00564,
CC ECO:0000269|PubMed:14767080}.
CC -!- DISRUPTION PHENOTYPE: Correct processing of the 3' end of 23S rRNA no
CC longer occurs in the absence of mrnC. {ECO:0000269|PubMed:19880604}.
CC -!- MISCELLANEOUS: Sulfate ions in the crystal structure may represent the
CC inorganic phosphate substrate. {ECO:0000305|PubMed:14767080}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000255|HAMAP-
CC Rule:MF_00564}.
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DR EMBL; M85163; AAA22705.1; -; Genomic_DNA.
DR EMBL; Z75208; CAA99554.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14797.1; -; Genomic_DNA.
DR PIR; A44914; A44914.
DR RefSeq; NP_390715.1; NC_000964.3.
DR RefSeq; WP_003246039.1; NZ_JNCM01000036.1.
DR PDB; 1OYP; X-ray; 2.76 A; A/B/C/D/E/F=1-245.
DR PDB; 1OYR; X-ray; 3.10 A; A/B/C/D/E/F=1-245.
DR PDB; 1OYS; X-ray; 2.40 A; A=1-245.
DR PDBsum; 1OYP; -.
DR PDBsum; 1OYR; -.
DR PDBsum; 1OYS; -.
DR AlphaFoldDB; P28619; -.
DR SMR; P28619; -.
DR STRING; 224308.BSU28370; -.
DR jPOST; P28619; -.
DR PaxDb; P28619; -.
DR PRIDE; P28619; -.
DR EnsemblBacteria; CAB14797; CAB14797; BSU_28370.
DR GeneID; 937463; -.
DR KEGG; bsu:BSU28370; -.
DR PATRIC; fig|224308.179.peg.3082; -.
DR eggNOG; COG0689; Bacteria.
DR InParanoid; P28619; -.
DR OMA; KGKGQGW; -.
DR PhylomeDB; P28619; -.
DR BioCyc; BSUB:BSU28370-MON; -.
DR EvolutionaryTrace; P28619; -.
DR PRO; PR:P28619; -.
DR Proteomes; UP000001570; 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:0031125; P:rRNA 3'-end processing; IMP:UniProtKB.
DR GO; GO:0016075; P:rRNA catabolic process; IBA:GO_Central.
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..245
FT /note="Ribonuclease PH"
FT /id="PRO_0000139869"
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:0000305|PubMed:14767080"
FT MUTAGEN 68..76
FT /note="RATNQRTIR->QATNQQTIQ: Protein crystallizes as a
FT dimer."
FT /evidence="ECO:0000269|PubMed:14767080"
FT STRAND 14..17
FT /evidence="ECO:0007829|PDB:1OYS"
FT STRAND 28..32
FT /evidence="ECO:0007829|PDB:1OYS"
FT STRAND 35..45
FT /evidence="ECO:0007829|PDB:1OYS"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:1OYS"
FT STRAND 52..55
FT /evidence="ECO:0007829|PDB:1OYP"
FT STRAND 58..64
FT /evidence="ECO:0007829|PDB:1OYS"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:1OYR"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:1OYR"
FT TURN 77..79
FT /evidence="ECO:0007829|PDB:1OYR"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:1OYR"
FT HELIX 86..100
FT /evidence="ECO:0007829|PDB:1OYS"
FT HELIX 104..107
FT /evidence="ECO:0007829|PDB:1OYS"
FT STRAND 111..120
FT /evidence="ECO:0007829|PDB:1OYS"
FT HELIX 125..146
FT /evidence="ECO:0007829|PDB:1OYS"
FT STRAND 149..152
FT /evidence="ECO:0007829|PDB:1OYS"
FT STRAND 159..167
FT /evidence="ECO:0007829|PDB:1OYS"
FT TURN 168..170
FT /evidence="ECO:0007829|PDB:1OYS"
FT STRAND 171..175
FT /evidence="ECO:0007829|PDB:1OYS"
FT HELIX 178..183
FT /evidence="ECO:0007829|PDB:1OYS"
FT STRAND 185..193
FT /evidence="ECO:0007829|PDB:1OYS"
FT STRAND 198..207
FT /evidence="ECO:0007829|PDB:1OYS"
FT HELIX 212..236
FT /evidence="ECO:0007829|PDB:1OYS"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:1OYP"
SQ SEQUENCE 245 AA; 26681 MW; D180DB086A5316B8 CRC64;
MRHDGRQHDE LRPITFDLDF ISHPEGSVLI TAGNTKVICN ASVEDRVPPF LRGGGKGWIT
AEYSMLPRAT NQRTIRESSK GKISGRTMEI QRLIGRALRA VVDLEKLGER TIWIDCDVIQ
ADGGTRTASI TGAFLAMAIA IGKLIKAGTI KTNPITDFLA AISVGIDKEQ GILLDLNYEE
DSSAEVDMNV IMTGSGRFVE LQGTGEEATF SREDLNGLLG LAEKGIQELI DKQKEVLGDS
LPELK
