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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
 
 
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