RNPH_BACAN
ID RNPH_BACAN Reviewed; 245 AA.
AC Q81LA9; Q6HSR4; Q6KM05;
DT 15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 124.
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};
GN OrderedLocusNames=BA_4715, GBAA_4715, BAS4377;
OS Bacillus anthracis.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=1392;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Ames / isolate Porton;
RX PubMed=12721629; DOI=10.1038/nature01586;
RA Read T.D., Peterson S.N., Tourasse N.J., Baillie L.W., Paulsen I.T.,
RA Nelson K.E., Tettelin H., Fouts D.E., Eisen J.A., Gill S.R.,
RA Holtzapple E.K., Okstad O.A., Helgason E., Rilstone J., Wu M.,
RA Kolonay J.F., Beanan M.J., Dodson R.J., Brinkac L.M., Gwinn M.L.,
RA DeBoy R.T., Madpu R., Daugherty S.C., Durkin A.S., Haft D.H., Nelson W.C.,
RA Peterson J.D., Pop M., Khouri H.M., Radune D., Benton J.L., Mahamoud Y.,
RA Jiang L., Hance I.R., Weidman J.F., Berry K.J., Plaut R.D., Wolf A.M.,
RA Watkins K.L., Nierman W.C., Hazen A., Cline R.T., Redmond C., Thwaite J.E.,
RA White O., Salzberg S.L., Thomason B., Friedlander A.M., Koehler T.M.,
RA Hanna P.C., Kolstoe A.-B., Fraser C.M.;
RT "The genome sequence of Bacillus anthracis Ames and comparison to closely
RT related bacteria.";
RL Nature 423:81-86(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Ames ancestor;
RX PubMed=18952800; DOI=10.1128/jb.01347-08;
RA Ravel J., Jiang L., Stanley S.T., Wilson M.R., Decker R.S., Read T.D.,
RA Worsham P., Keim P.S., Salzberg S.L., Fraser-Liggett C.M., Rasko D.A.;
RT "The complete genome sequence of Bacillus anthracis Ames 'Ancestor'.";
RL J. Bacteriol. 191:445-446(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Sterne;
RA Brettin T.S., Bruce D., Challacombe J.F., Gilna P., Han C., Hill K.,
RA Hitchcock P., Jackson P., Keim P., Longmire J., Lucas S., Okinaka R.,
RA Richardson P., Rubin E., Tice H.;
RT "Complete genome sequence of Bacillus anthracis Sterne.";
RL Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0007744|PDB:3DD6}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, AND
RP SUBUNIT.
RC STRAIN=Ames;
RX PubMed=19153445; DOI=10.1107/s1744309108041511;
RA Rawlings A.E., Blagova E.V., Levdikov V.M., Fogg M.J., Wilson K.S.,
RA Wilkinson A.J.;
RT "The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7 A
RT resolution.";
RL Acta Crystallogr. F 65:2-7(2009).
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:19153445). {ECO:0000255|HAMAP-Rule:MF_00564,
CC ECO:0000305|PubMed:19153445}.
CC -!- MISCELLANEOUS: Sulfate ions in the crystal structure may represent the
CC inorganic phosphate substrate. {ECO:0000305|PubMed:19153445}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000255|HAMAP-
CC Rule:MF_00564}.
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DR EMBL; AE016879; AAP28413.1; -; Genomic_DNA.
DR EMBL; AE017334; AAT33839.1; -; Genomic_DNA.
DR EMBL; AE017225; AAT56675.1; -; Genomic_DNA.
DR RefSeq; NP_846927.1; NC_003997.3.
DR RefSeq; WP_001261764.1; NZ_WXXJ01000001.1.
DR RefSeq; YP_030624.1; NC_005945.1.
DR PDB; 3DD6; X-ray; 1.70 A; A=1-245.
DR PDBsum; 3DD6; -.
DR AlphaFoldDB; Q81LA9; -.
DR SMR; Q81LA9; -.
DR IntAct; Q81LA9; 1.
DR STRING; 260799.BAS4377; -.
DR DNASU; 1088544; -.
DR EnsemblBacteria; AAP28413; AAP28413; BA_4715.
DR EnsemblBacteria; AAT33839; AAT33839; GBAA_4715.
DR GeneID; 45024354; -.
DR KEGG; ban:BA_4715; -.
DR KEGG; bar:GBAA_4715; -.
DR KEGG; bat:BAS4377; -.
DR PATRIC; fig|198094.11.peg.4680; -.
DR eggNOG; COG0689; Bacteria.
DR HOGENOM; CLU_050858_0_0_9; -.
DR OMA; KGKGQGW; -.
DR EvolutionaryTrace; Q81LA9; -.
DR Proteomes; UP000000427; Chromosome.
DR Proteomes; UP000000594; 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; 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; -; 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_0000139862"
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 ECO:0000305|PubMed:19153445"
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:19153445"
FT STRAND 14..19
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 21..32
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 35..45
FT /evidence="ECO:0007829|PDB:3DD6"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 58..65
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:3DD6"
FT HELIX 85..101
FT /evidence="ECO:0007829|PDB:3DD6"
FT HELIX 104..107
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 111..120
FT /evidence="ECO:0007829|PDB:3DD6"
FT HELIX 125..146
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 149..152
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 159..167
FT /evidence="ECO:0007829|PDB:3DD6"
FT TURN 168..170
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 171..175
FT /evidence="ECO:0007829|PDB:3DD6"
FT HELIX 178..182
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 184..193
FT /evidence="ECO:0007829|PDB:3DD6"
FT STRAND 198..208
FT /evidence="ECO:0007829|PDB:3DD6"
FT HELIX 212..237
FT /evidence="ECO:0007829|PDB:3DD6"
FT HELIX 238..243
FT /evidence="ECO:0007829|PDB:3DD6"
SQ SEQUENCE 245 AA; 26983 MW; 00053DA2C582D0E6 CRC64;
MRVDGREKTE LRHIHIHTNY LKHPEGSVLI EVGDTKVICS ATIEERVPPF MRGEGKGWVT
AEYAMIPRAT EQRTIRESSK GKVTGRTMEI QRLIGRALRA VVDLEALGER TVWIDCDVIQ
ADGGTRTASI TGAYVAMVLA FEKLLQAEKV SKIPVKDYLA ATSVGIVEEQ GVVLDLNYAE
DSKADVDMNV IMTGKGQFVE VQGTGEEATF SRAQLNELLD AAEQGIFQLI DIQKEALGDI
VSHIE
