(data stored in SCRATCH zone)

SWISSPROT: RNM5_BACSU

ID   RNM5_BACSU              Reviewed;         186 AA.
AC   P37547;
DT   01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1994, sequence version 1.
DT   11-DEC-2019, entry version 118.
DE   RecName: Full=Ribonuclease M5 {ECO:0000255|HAMAP-Rule:MF_01469};
DE            EC=3.1.26.8 {ECO:0000255|HAMAP-Rule:MF_01469};
DE   AltName: Full=RNase M5 {ECO:0000255|HAMAP-Rule:MF_01469};
DE   AltName: Full=Ribosomal RNA terminal maturase M5 {ECO:0000255|HAMAP-Rule:MF_01469};
GN   Name=rnmV {ECO:0000255|HAMAP-Rule:MF_01469}; Synonyms=yabF;
GN   OrderedLocusNames=BSU00410;
OS   Bacillus subtilis (strain 168).
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX   NCBI_TaxID=224308;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=168;
RX   PubMed=7584024; DOI=10.1093/dnares/1.1.1;
RA   Ogasawara N., Nakai S., Yoshikawa H.;
RT   "Systematic sequencing of the 180 kilobase region of the Bacillus subtilis
RT   chromosome containing the replication origin.";
RL   DNA Res. 1:1-14(1994).
RN   [2]
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   [3]
RP   PROTEIN SEQUENCE OF 1-5, IDENTIFICATION AS RNASE M5, SUBCELLULAR LOCATION,
RP   RIBOSOME ASSOCIATION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=168;
RX   PubMed=11233981; DOI=10.1017/s1355838201002163;
RA   Condon C., Brechemier-Baey D., Beltchev B., Grunberg-Manago M., Putzer H.;
RT   "Identification of the gene encoding the 5S ribosomal RNA maturase in
RT   Bacillus subtilis: mature 5S rRNA is dispensable for ribosome function.";
RL   RNA 7:242-253(2001).
RN   [4]
RP   FUNCTION AS AN ENDORIBONUCLEASE.
RC   STRAIN=168;
RX   PubMed=4215038; DOI=10.1038/252598a0;
RA   Sogin M.L., Pace N.R.;
RT   "In vitro maturation of precursors of 5S ribosomal RNA from Bacillus
RT   subtilis.";
RL   Nature 252:598-600(1974).
RN   [5]
RP   FUNCTION AS AN ENDORIBONUCLEASE, PH DEPENDENCE, COFACTOR, SUBCELLULAR
RP   LOCATION, RIBOSOME ASSOCIATION, AND SUBUNIT.
RC   STRAIN=168;
RX   PubMed=402365;
RA   Sogin M.L., Pace B., Pace N.R.;
RT   "Partial purification and properties of a ribosomal RNA maturation
RT   endonuclease from Bacillus subtilis.";
RL   J. Biol. Chem. 252:1350-1357(1977).
RN   [6]
RP   REQUIREMENT FOR RIBOSOMAL PROTEIN L18.
RX   PubMed=6432797;
RA   Stahl D.A., Pace B., Marsh T., Pace N.R.;
RT   "The ribonucleoprotein substrate for a ribosomal RNA-processing nuclease.";
RL   J. Biol. Chem. 259:11448-11453(1984).
RN   [7]
RP   RRNA-BINDING, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF GLU-10; GLY-11;
RP   GLY-31; ASP-56; ASP-58; GLY-61; ARG-65; LEU-107 AND 140-ARG--GLU-142.
RX   PubMed=16077031; DOI=10.1093/nar/gki752;
RA   Allemand F., Mathy N., Brechemier-Baey D., Condon C.;
RT   "The 5S rRNA maturase, ribonuclease M5, is a Toprim domain family member.";
RL   Nucleic Acids Res. 33:4368-4376(2005).
CC   -!- FUNCTION: Required for correct processing of both the 5' and 3' ends of
CC       5S rRNA precursor. Cleaves both sides of a double-stranded region
CC       yielding mature 5S rRNA in one step. Releases 5'-phosphoryl and 3'-
CC       hydroxy termini. {ECO:0000255|HAMAP-Rule:MF_01469,
CC       ECO:0000269|PubMed:402365, ECO:0000269|PubMed:4215038}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endonucleolytic cleavage of RNA, removing 21 and 42
CC         nucleotides, respectively, from the 5'- and 3'-termini of a 5S-rRNA
CC         precursor.; EC=3.1.26.8; Evidence={ECO:0000255|HAMAP-Rule:MF_01469};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:402365};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:402365};
CC       Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC         Evidence={ECO:0000269|PubMed:402365};
CC       Note=Divalent metal cations; Mg(2+) > Mn(2+) > Ca(2+).
CC       {ECO:0000269|PubMed:402365};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 7-8.5 at 37 degrees Celsius.
CC         {ECO:0000269|PubMed:402365};
CC   -!- SUBUNIT: Requires ribosomal protein L18 (rplR) for catalysis; it can be
CC       replaced by 30% dimethylsulfoxide suggesting L18 functions as an rRNA
CC       folding chaperone. {ECO:0000269|PubMed:402365}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01469,
CC       ECO:0000269|PubMed:11233981, ECO:0000269|PubMed:402365}.
CC       Note=Associated with 70S ribosomes.
CC   -!- DISRUPTION PHENOTYPE: Not essential. Accumulation of precursor forms of
CC       5S rRNA in total, ribosomes and polysome RNA preparations; smaller
CC       forms (126 and 135 nucleotides) are predominantly found in ribosomes
CC       and polysomes. Each of the 10 rrn operons gives rise to a different 5S
CC       rRNA precursor due to differences in their 3' ends.
CC       {ECO:0000269|PubMed:11233981, ECO:0000269|PubMed:16077031}.
CC   -!- SIMILARITY: Belongs to the ribonuclease M5 family. {ECO:0000255|HAMAP-
CC       Rule:MF_01469}.
DR   EMBL; D26185; BAA05276.1; -; Genomic_DNA.
DR   EMBL; AL009126; CAB11817.1; -; Genomic_DNA.
DR   PIR; S66070; S66070.
DR   RefSeq; NP_387922.1; NC_000964.3.
DR   RefSeq; WP_003226752.1; NZ_JNCM01000028.1.
DR   SMR; P37547; -.
DR   STRING; 224308.BSU00410; -.
DR   PaxDb; P37547; -.
DR   PRIDE; P37547; -.
DR   EnsemblBacteria; CAB11817; CAB11817; BSU00410.
DR   GeneID; 937001; -.
DR   KEGG; bsu:BSU00410; -.
DR   PATRIC; fig|224308.179.peg.41; -.
DR   eggNOG; COG1658; LUCA.
DR   HOGENOM; HOG000203762; -.
DR   InParanoid; P37547; -.
DR   KO; K05985; -.
DR   OMA; RLQMFQI; -.
DR   PhylomeDB; P37547; -.
DR   BioCyc; BSUB:BSU00410-MONOMER; -.
DR   SABIO-RK; P37547; -.
DR   Proteomes; UP000001570; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0043822; F:ribonuclease M5 activity; IDA:UniProtKB.
DR   GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0042254; P:ribosome biogenesis; IMP:UniProtKB.
DR   GO; GO:0006364; P:rRNA processing; IDA:UniProtKB.
DR   CDD; cd01027; TOPRIM_RNase_M5_like; 1.
DR   HAMAP; MF_01469; RNase_M5; 1.
DR   InterPro; IPR004466; RNase_M5.
DR   InterPro; IPR025156; RNase_M5_C.
DR   InterPro; IPR006171; TOPRIM_domain.
DR   InterPro; IPR034141; TOPRIM_RNase_M5-like.
DR   Pfam; PF13331; DUF4093; 1.
DR   Pfam; PF13662; Toprim_4; 1.
DR   SMART; SM00493; TOPRIM; 1.
DR   TIGRFAMs; TIGR00334; 5S_RNA_mat_M5; 1.
DR   PROSITE; PS50880; TOPRIM; 1.
PE   1: Evidence at protein level;
DR   PRODOM; P37547.
DR   SWISS-2DPAGE; P37547.
KW   Cytoplasm; Direct protein sequencing; Endonuclease; Hydrolase; Magnesium;
KW   Metal-binding; Nuclease; Reference proteome; Ribosome biogenesis;
KW   RNA-binding; rRNA processing; rRNA-binding.
FT   CHAIN           1..186
FT                   /note="Ribonuclease M5"
FT                   /id="PRO_0000049440"
FT   DOMAIN          4..94
FT                   /note="Toprim"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01469"
FT   METAL           10
FT                   /note="Magnesium 1; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01469"
FT   METAL           56
FT                   /note="Magnesium 1; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01469"
FT   METAL           56
FT                   /note="Magnesium 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01469"
FT   METAL           58
FT                   /note="Magnesium 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01469"
FT   MUTAGEN         10
FT                   /note="E->A: Loss of activity, 50% rRNA-binding."
FT                   /evidence="ECO:0000269|PubMed:16077031"
FT   MUTAGEN         11
FT                   /note="G->A: 30-fold loss of activity."
FT                   /evidence="ECO:0000269|PubMed:16077031"
FT   MUTAGEN         31
FT                   /note="G->A: Loss of activity."
FT                   /evidence="ECO:0000269|PubMed:16077031"
FT   MUTAGEN         56
FT                   /note="D->A: Loss of activity, rRNA-binding normal."
FT                   /evidence="ECO:0000269|PubMed:16077031"
FT   MUTAGEN         58
FT                   /note="D->A: Loss of activity, rRNA-binding normal."
FT                   /evidence="ECO:0000269|PubMed:16077031"
FT   MUTAGEN         61
FT                   /note="G->A: Loss of activity in vivo, about 100-fold loss
FT                   in vitro."
FT                   /evidence="ECO:0000269|PubMed:16077031"
FT   MUTAGEN         65
FT                   /note="R->A: 100-fold loss of activity."
FT                   /evidence="ECO:0000269|PubMed:16077031"
FT   MUTAGEN         107
FT                   /note="L->A: 10-fold loss of activity."
FT                   /evidence="ECO:0000269|PubMed:16077031"
FT   MUTAGEN         140..142
FT                   /note="Missing: Loss of activity, significant loss of rRNA
FT                   binding."
FT                   /evidence="ECO:0000269|PubMed:16077031"
SQ   SEQUENCE   186 AA;  20674 MW;  CE18BC3D9F9C2F81 CRC64;
     MKIKEIIVVE GRDDTARIKL AVDADTIETN GSAIDDHVID QIRLAQKTRG VIILTDPDFP
     GEKIRKTISE AVPGCKHAFL PKHLAKPKNK RGIGVEHASV ESIRACLENV HEEMEAQPSD
     ISAEDLIHAG LIGGPAAKCR RERLGDLLKI GYTNGKQLQK RLQMFQIKKS DFMSALDTVM
     REEQNE
//

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