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 03-AUG-2022, entry version 147.
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 P54548; P54548: rnz; NbExp=2; IntAct=EBI-15572938, EBI-15572938;
CC -!- SIMILARITY: Belongs to the RNase Z family. {ECO:0000255|HAMAP-
CC Rule:MF_01818}.
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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 AlphaFoldDB; P54548; -.
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; BSU_23840.
DR GeneID; 938694; -.
DR KEGG; bsu:BSU23840; -.
DR PATRIC; fig|224308.179.peg.2597; -.
DR eggNOG; COG1234; Bacteria.
DR InParanoid; P54548; -.
DR OMA; GTQRQMM; -.
DR PhylomeDB; P54548; -.
DR BioCyc; BSUB:BSU23840-MON; -.
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 GO; GO:0042779; P:tRNA 3'-trailer cleavage; IBA:GO_Central.
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;
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 BINDING 63
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:15654328"
FT BINDING 65
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:15654328"
FT BINDING 67
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:15654328, ECO:0000269|PubMed:16518398"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:15654328, ECO:0000269|PubMed:16518398"
FT BINDING 140
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:15654328"
FT BINDING 211
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:15654328"
FT BINDING 211
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:15654328, ECO:0000269|PubMed:16518398"
FT BINDING 269
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="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:0007829|PDB:1Y44"
FT STRAND 9..12
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 21..25
FT /evidence="ECO:0007829|PDB:1Y44"
FT TURN 27..30
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 31..36
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 42..46
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 53..55
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 56..60
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:1Y44"
FT TURN 69..71
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 72..81
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 88..93
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 96..106
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 115..119
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 122..127
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 129..137
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 139..151
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 160..165
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 172..178
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 182..184
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 190..192
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 193..196
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 205..208
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 216..221
FT /evidence="ECO:0007829|PDB:1Y44"
FT TURN 222..224
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 226..231
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 239..244
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 250..260
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 263..268
FT /evidence="ECO:0007829|PDB:1Y44"
FT HELIX 278..289
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 291..295
FT /evidence="ECO:0007829|PDB:1Y44"
FT STRAND 301..303
FT /evidence="ECO:0007829|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
