(data stored in SCRATCH zone)

SWISSPROT: RNZ_BACSU

ID   RNZ_BACSU               Reviewed;         307 AA.
AC   P54548;
DT   01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1996, sequence version 1.
DT   11-DEC-2019, entry version 138.
DE   RecName: Full=Ribonuclease Z {ECO:0000255|HAMAP-Rule:MF_01818};
DE            Short=RNase Z {ECO:0000255|HAMAP-Rule:MF_01818};
DE            EC=3.1.26.11 {ECO:0000255|HAMAP-Rule:MF_01818, ECO:0000269|PubMed:12941704};
DE   AltName: Full=tRNA 3 endonuclease {ECO:0000255|HAMAP-Rule:MF_01818};
DE   AltName: Full=tRNase Z {ECO:0000255|HAMAP-Rule:MF_01818};
GN   Name=rnz {ECO:0000255|HAMAP-Rule:MF_01818}; Synonyms=yqjK;
GN   OrderedLocusNames=BSU23840;
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 / JH642;
RX   PubMed=8969508; DOI=10.1099/13500872-142-11-3103;
RA   Mizuno M., Masuda S., Takemaru K., Hosono S., Sato T., Takeuchi M.,
RA   Kobayashi Y.;
RT   "Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the
RT   Bacillus subtilis genome containing the skin element and many sporulation
RT   genes.";
RL   Microbiology 142:3103-3111(1996).
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   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=12941704; DOI=10.1093/emboj/cdg435;
RA   Pellegrini O., Nezzar J., Marchfelder A., Putzer H., Condon C.;
RT   "Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in
RT   Bacillus subtilis.";
RL   EMBO J. 22:4534-4543(2003).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH ZINC IONS, ACTIVE
RP   SITE, ENZYME MECHANISM, SUBUNIT, AND COFACTOR.
RX   PubMed=15654328; DOI=10.1038/nature03284;
RA   de la Sierra-Gallay I.L., Pellegrini O., Condon C.;
RT   "Structural basis for substrate binding, cleavage and allostery in the tRNA
RT   maturase RNase Z.";
RL   Nature 433:657-661(2005).
RN   [5]
RP   X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH TRNA AND ZINC ION,
RP   AND COFACTOR.
RX   PubMed=16518398; DOI=10.1038/nsmb1066;
RA   Li de la Sierra-Gallay I., Mathy N., Pellegrini O., Condon C.;
RT   "Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer
RT   RNA.";
RL   Nat. Struct. Mol. Biol. 13:376-377(2006).
CC   -!- FUNCTION: Zinc phosphodiesterase, which displays some tRNA 3'-
CC       processing endonuclease activity. Probably involved in tRNA maturation,
CC       by removing a 3'-trailer from precursor tRNA. {ECO:0000255|HAMAP-
CC       Rule:MF_01818, ECO:0000269|PubMed:12941704}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endonucleolytic cleavage of RNA, removing extra 3' nucleotides
CC         from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy
CC         group is left at the tRNA terminus and a 5'-phosphoryl group is left
CC         at the trailer molecule.; EC=3.1.26.11; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_01818, ECO:0000269|PubMed:12941704};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000269|PubMed:15654328, ECO:0000269|PubMed:16518398};
CC       Note=Binds 2 Zn(2+) ions. {ECO:0000269|PubMed:15654328};
CC   -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01818,
CC       ECO:0000269|PubMed:15654328, ECO:0000269|PubMed:16518398}.
CC   -!- INTERACTION:
CC       Self; NbExp=2; IntAct=EBI-15572938, EBI-15572938;
CC   -!- SIMILARITY: Belongs to the RNase Z family. {ECO:0000255|HAMAP-
CC       Rule:MF_01818}.
DR   EMBL; D84432; BAA12617.1; -; Genomic_DNA.
DR   EMBL; AL009126; CAB14316.1; -; Genomic_DNA.
DR   PIR; C69964; C69964.
DR   RefSeq; NP_390265.1; NC_000964.3.
DR   RefSeq; WP_004398681.1; NZ_JNCM01000036.1.
DR   PDB; 1Y44; X-ray; 2.10 A; A/B=1-307.
DR   PDB; 2FK6; X-ray; 2.90 A; A=1-307.
DR   PDB; 4GCW; X-ray; 3.00 A; A=1-307.
DR   PDBsum; 1Y44; -.
DR   PDBsum; 2FK6; -.
DR   PDBsum; 4GCW; -.
DR   SMR; P54548; -.
DR   DIP; DIP-29070N; -.
DR   STRING; 224308.BSU23840; -.
DR   DrugBank; DB03814; 2-(N-Morpholino)-Ethanesulfonic Acid.
DR   PaxDb; P54548; -.
DR   PRIDE; P54548; -.
DR   EnsemblBacteria; CAB14316; CAB14316; BSU23840.
DR   GeneID; 938694; -.
DR   KEGG; bsu:BSU23840; -.
DR   PATRIC; fig|224308.179.peg.2597; -.
DR   eggNOG; ENOG4105IES; Bacteria.
DR   eggNOG; COG1234; LUCA.
DR   HOGENOM; HOG000272419; -.
DR   InParanoid; P54548; -.
DR   KO; K00784; -.
DR   OMA; HNGYLLR; -.
DR   PhylomeDB; P54548; -.
DR   BioCyc; BSUB:BSU23840-MONOMER; -.
DR   BRENDA; 3.1.26.11; 658.
DR   EvolutionaryTrace; P54548; -.
DR   Proteomes; UP000001570; Chromosome.
DR   GO; GO:0042781; F:3'-tRNA processing endoribonuclease activity; IBA:GO_Central.
DR   GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR   GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR   CDD; cd07717; RNaseZ_ZiPD-like_MBL-fold; 1.
DR   Gene3D; 3.60.15.10; -; 1.
DR   HAMAP; MF_01818; RNase_Z_BN; 1.
DR   InterPro; IPR001279; Metallo-B-lactamas.
DR   InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR   InterPro; IPR013471; RNase_Z/BN.
DR   Pfam; PF12706; Lactamase_B_2; 2.
DR   SMART; SM00849; Lactamase_B; 1.
DR   SUPFAM; SSF56281; SSF56281; 1.
DR   TIGRFAMs; TIGR02651; RNase_Z; 1.
PE   1: Evidence at protein level;
DR   PRODOM; P54548.
DR   SWISS-2DPAGE; P54548.
KW   3D-structure; Endonuclease; Hydrolase; Metal-binding; Nuclease;
KW   Reference proteome; tRNA processing; Zinc.
FT   CHAIN           1..307
FT                   /note="Ribonuclease Z"
FT                   /id="PRO_0000155849"
FT   ACT_SITE        67
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT                   ECO:0000305|PubMed:15654328"
FT   METAL           63
FT                   /note="Zinc 1; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT                   ECO:0000269|PubMed:15654328"
FT   METAL           65
FT                   /note="Zinc 1; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT                   ECO:0000269|PubMed:15654328"
FT   METAL           67
FT                   /note="Zinc 2; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT                   ECO:0000269|PubMed:15654328, ECO:0000269|PubMed:16518398"
FT   METAL           68
FT                   /note="Zinc 2; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT                   ECO:0000269|PubMed:15654328, ECO:0000269|PubMed:16518398"
FT   METAL           140
FT                   /note="Zinc 1; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT                   ECO:0000269|PubMed:15654328"
FT   METAL           211
FT                   /note="Zinc 1; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT                   ECO:0000269|PubMed:15654328"
FT   METAL           211
FT                   /note="Zinc 2; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT                   ECO:0000269|PubMed:15654328, ECO:0000269|PubMed:16518398"
FT   METAL           269
FT                   /note="Zinc 2; catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT                   ECO:0000269|PubMed:15654328, ECO:0000269|PubMed:16518398"
FT   STRAND          2..7
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          9..12
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          21..25
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   TURN            27..30
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          31..36
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           42..46
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           53..55
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          56..60
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           66..68
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   TURN            69..71
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           72..81
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          88..93
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           96..106
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          115..119
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          122..127
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          129..137
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          139..151
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           160..165
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           172..178
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          182..184
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          190..192
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           193..196
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          205..208
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           216..221
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   TURN            222..224
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          226..231
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           239..244
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           250..260
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          263..268
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   HELIX           278..289
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          291..295
FT                   /evidence="ECO:0000244|PDB:1Y44"
FT   STRAND          301..303
FT                   /evidence="ECO:0000244|PDB:1Y44"
SQ   SEQUENCE   307 AA;  34023 MW;  6E03CA54C55D7C84 CRC64;
     MELLFLGTGA GIPAKARNVT SVALKLLEER RSVWLFDCGE ATQHQILHTT IKPRKIEKIF
     ITHMHGDHVY GLPGLLGSRS FQGGEDELTV YGPKGIKAFI ETSLAVTKTH LTYPLAIQEI
     EEGIVFEDDQ FIVTAVSVIH GVEAFGYRVQ EKDVPGSLKA DVLKEMNIPP GPVYQKIKKG
     ETVTLEDGRI INGNDFLEPP KKGRSVVFSG DTRVSDKLKE LARDCDVLVH EATFAKEDRK
     LAYDYYHSTT EQAAVTAKEA RAKQLILTHI SARYQGDASL ELQKEAVDVF PNSVAAYDFL
     EVNVPRG
//

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