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Protein

Ribonuclease Z

Gene

rnz

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.UniRule annotation1 Publication

Catalytic activityi

Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule.UniRule annotation1 Publication

Cofactori

Zn2+2 PublicationsNote: Binds 2 Zn2+ ions.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi63 – 631Zinc 1; catalyticUniRule annotation1 Publication
Metal bindingi65 – 651Zinc 1; catalyticUniRule annotation1 Publication
Active sitei67 – 671Proton acceptorUniRule annotation1 Publication
Metal bindingi67 – 671Zinc 2; catalyticUniRule annotation2 Publications
Metal bindingi68 – 681Zinc 2; catalyticUniRule annotation2 Publications
Metal bindingi140 – 1401Zinc 1; catalyticUniRule annotation1 Publication
Metal bindingi211 – 2111Zinc 1; catalyticUniRule annotation1 Publication
Metal bindingi211 – 2111Zinc 2; catalyticUniRule annotation2 Publications
Metal bindingi269 – 2691Zinc 2; catalyticUniRule annotation2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciBSUB:BSU23840-MONOMER.
BRENDAi3.1.26.11. 658.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease ZUniRule annotation (EC:3.1.26.11UniRule annotation1 Publication)
Short name:
RNase ZUniRule annotation
Alternative name(s):
tRNA 3 endonucleaseUniRule annotation
tRNase ZUniRule annotation
Gene namesi
Name:rnzUniRule annotation
Synonyms:yqjK
Ordered Locus Names:BSU23840
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 307307Ribonuclease ZPRO_0000155849Add
BLAST

Proteomic databases

PaxDbiP54548.

Interactioni

Subunit structurei

Homodimer.UniRule annotation2 Publications

Protein-protein interaction databases

DIPiDIP-29070N.
STRINGi224308.Bsubs1_010100013081.

Structurei

Secondary structure

1
307
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76Combined sources
Beta strandi9 – 124Combined sources
Beta strandi21 – 255Combined sources
Turni27 – 304Combined sources
Beta strandi31 – 366Combined sources
Helixi42 – 465Combined sources
Helixi53 – 553Combined sources
Beta strandi56 – 605Combined sources
Helixi66 – 683Combined sources
Turni69 – 713Combined sources
Helixi72 – 8110Combined sources
Beta strandi88 – 936Combined sources
Helixi96 – 10611Combined sources
Beta strandi115 – 1195Combined sources
Beta strandi122 – 1276Combined sources
Beta strandi129 – 1379Combined sources
Beta strandi139 – 15113Combined sources
Helixi160 – 1656Combined sources
Helixi172 – 1787Combined sources
Beta strandi182 – 1843Combined sources
Beta strandi190 – 1923Combined sources
Helixi193 – 1964Combined sources
Beta strandi205 – 2084Combined sources
Helixi216 – 2216Combined sources
Turni222 – 2243Combined sources
Beta strandi226 – 2316Combined sources
Helixi239 – 2446Combined sources
Helixi250 – 26011Combined sources
Beta strandi263 – 2686Combined sources
Helixi278 – 28912Combined sources
Beta strandi291 – 2955Combined sources
Beta strandi301 – 3033Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Y44X-ray2.10A/B1-307[»]
2FK6X-ray2.90A1-307[»]
4GCWX-ray3.00A1-307[»]
ProteinModelPortaliP54548.
SMRiP54548. Positions 1-307.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP54548.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase Z family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105IES. Bacteria.
COG1234. LUCA.
HOGENOMiHOG000272419.
InParanoidiP54548.
KOiK00784.
OMAiWYLVDCG.
OrthoDBiEOG61P6TK.
PhylomeDBiP54548.

Family and domain databases

Gene3Di3.60.15.10. 2 hits.
HAMAPiMF_01818. RNase_Z_BN.
InterProiIPR001279. Metallo-B-lactamas.
IPR013471. RNase_Z/BN.
[Graphical view]
PfamiPF12706. Lactamase_B_2. 2 hits.
[Graphical view]
SMARTiSM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.
TIGRFAMsiTIGR02651. RNase_Z. 1 hit.

Sequencei

Sequence statusi: Complete.

P54548-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELLFLGTGA GIPAKARNVT SVALKLLEER RSVWLFDCGE ATQHQILHTT
60 70 80 90 100
IKPRKIEKIF ITHMHGDHVY GLPGLLGSRS FQGGEDELTV YGPKGIKAFI
110 120 130 140 150
ETSLAVTKTH LTYPLAIQEI EEGIVFEDDQ FIVTAVSVIH GVEAFGYRVQ
160 170 180 190 200
EKDVPGSLKA DVLKEMNIPP GPVYQKIKKG ETVTLEDGRI INGNDFLEPP
210 220 230 240 250
KKGRSVVFSG DTRVSDKLKE LARDCDVLVH EATFAKEDRK LAYDYYHSTT
260 270 280 290 300
EQAAVTAKEA RAKQLILTHI SARYQGDASL ELQKEAVDVF PNSVAAYDFL

EVNVPRG
Length:307
Mass (Da):34,023
Last modified:October 1, 1996 - v1
Checksum:i6E03CA54C55D7C84
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D84432 Genomic DNA. Translation: BAA12617.1.
AL009126 Genomic DNA. Translation: CAB14316.1.
PIRiC69964.
RefSeqiNP_390265.1. NC_000964.3.
WP_004398681.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB14316; CAB14316; BSU23840.
GeneIDi938694.
KEGGibsu:BSU23840.
PATRICi18976593. VBIBacSub10457_2487.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D84432 Genomic DNA. Translation: BAA12617.1.
AL009126 Genomic DNA. Translation: CAB14316.1.
PIRiC69964.
RefSeqiNP_390265.1. NC_000964.3.
WP_004398681.1. NZ_JNCM01000036.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Y44X-ray2.10A/B1-307[»]
2FK6X-ray2.90A1-307[»]
4GCWX-ray3.00A1-307[»]
ProteinModelPortaliP54548.
SMRiP54548. Positions 1-307.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-29070N.
STRINGi224308.Bsubs1_010100013081.

Proteomic databases

PaxDbiP54548.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14316; CAB14316; BSU23840.
GeneIDi938694.
KEGGibsu:BSU23840.
PATRICi18976593. VBIBacSub10457_2487.

Phylogenomic databases

eggNOGiENOG4105IES. Bacteria.
COG1234. LUCA.
HOGENOMiHOG000272419.
InParanoidiP54548.
KOiK00784.
OMAiWYLVDCG.
OrthoDBiEOG61P6TK.
PhylomeDBiP54548.

Enzyme and pathway databases

BioCyciBSUB:BSU23840-MONOMER.
BRENDAi3.1.26.11. 658.

Miscellaneous databases

EvolutionaryTraceiP54548.

Family and domain databases

Gene3Di3.60.15.10. 2 hits.
HAMAPiMF_01818. RNase_Z_BN.
InterProiIPR001279. Metallo-B-lactamas.
IPR013471. RNase_Z/BN.
[Graphical view]
PfamiPF12706. Lactamase_B_2. 2 hits.
[Graphical view]
SMARTiSM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.
TIGRFAMsiTIGR02651. RNase_Z. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the Bacillus subtilis genome containing the skin element and many sporulation genes."
    Mizuno M., Masuda S., Takemaru K., Hosono S., Sato T., Takeuchi M., Kobayashi Y.
    Microbiology 142:3103-3111(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / JH642.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis."
    Pellegrini O., Nezzar J., Marchfelder A., Putzer H., Condon C.
    EMBO J. 22:4534-4543(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  4. "Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z."
    de la Sierra-Gallay I.L., Pellegrini O., Condon C.
    Nature 433:657-661(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH ZINC IONS, ACTIVE SITE, ENZYME MECHANISM, SUBUNIT, COFACTOR.
  5. "Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA."
    Li de la Sierra-Gallay I., Mathy N., Pellegrini O., Condon C.
    Nat. Struct. Mol. Biol. 13:376-377(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH TRNA AND ZINC ION, COFACTOR.

Entry informationi

Entry nameiRNZ_BACSU
AccessioniPrimary (citable) accession number: P54548
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: May 11, 2016
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.