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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)DescriptionActionsGraphical viewLength
Metal bindingi63Zinc 1; catalyticUniRule annotation1 Publication1
Metal bindingi65Zinc 1; catalyticUniRule annotation1 Publication1
Active sitei67Proton acceptorUniRule annotation1 Publication1
Metal bindingi67Zinc 2; catalyticUniRule annotation2 Publications1
Metal bindingi68Zinc 2; catalyticUniRule annotation2 Publications1
Metal bindingi140Zinc 1; catalyticUniRule annotation1 Publication1
Metal bindingi211Zinc 1; catalyticUniRule annotation1 Publication1
Metal bindingi211Zinc 2; catalyticUniRule annotation2 Publications1
Metal bindingi269Zinc 2; catalyticUniRule annotation2 Publications1

GO - Molecular functioni

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001558491 – 307Ribonuclease ZAdd BLAST307

Proteomic databases

PaxDbiP54548.

Interactioni

Subunit structurei

Homodimer.UniRule annotation2 Publications

Protein-protein interaction databases

DIPiDIP-29070N.
STRINGi224308.Bsubs1_010100013081.

Structurei

Secondary structure

1307
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Beta strandi9 – 12Combined sources4
Beta strandi21 – 25Combined sources5
Turni27 – 30Combined sources4
Beta strandi31 – 36Combined sources6
Helixi42 – 46Combined sources5
Helixi53 – 55Combined sources3
Beta strandi56 – 60Combined sources5
Helixi66 – 68Combined sources3
Turni69 – 71Combined sources3
Helixi72 – 81Combined sources10
Beta strandi88 – 93Combined sources6
Helixi96 – 106Combined sources11
Beta strandi115 – 119Combined sources5
Beta strandi122 – 127Combined sources6
Beta strandi129 – 137Combined sources9
Beta strandi139 – 151Combined sources13
Helixi160 – 165Combined sources6
Helixi172 – 178Combined sources7
Beta strandi182 – 184Combined sources3
Beta strandi190 – 192Combined sources3
Helixi193 – 196Combined sources4
Beta strandi205 – 208Combined sources4
Helixi216 – 221Combined sources6
Turni222 – 224Combined sources3
Beta strandi226 – 231Combined sources6
Helixi239 – 244Combined sources6
Helixi250 – 260Combined sources11
Beta strandi263 – 268Combined sources6
Helixi278 – 289Combined sources12
Beta strandi291 – 295Combined sources5
Beta strandi301 – 303Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Y44X-ray2.10A/B1-307[»]
2FK6X-ray2.90A1-307[»]
4GCWX-ray3.00A1-307[»]
ProteinModelPortaliP54548.
SMRiP54548.
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.
PhylomeDBiP54548.

Family and domain databases

Gene3Di3.60.15.10. 2 hits.
HAMAPiMF_01818. RNase_Z_BN. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Y44X-ray2.10A/B1-307[»]
2FK6X-ray2.90A1-307[»]
4GCWX-ray3.00A1-307[»]
ProteinModelPortaliP54548.
SMRiP54548.
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.
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. 1 hit.
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...

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: November 2, 2016
This is version 124 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.