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Protein

Ribonuclease 3

Gene

RNT1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. In vitro, cleaves synthetic 5'-ETS RNA A0 site in the absence of snoRNA or other factors. Has an essential growth function in addition to pre-rRNA processing.

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphomonoester.

GO - Molecular functioni

  • ribonuclease III activity Source: SGD
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • box C/D snoRNA processing Source: SGD
  • box H/ACA snoRNA processing Source: SGD
  • chromatin organization Source: SGD
  • mRNA cleavage Source: SGD
  • regulation of fungal-type cell wall organization Source: SGD
  • RNA phosphodiester bond hydrolysis Source: GOC
  • RNA phosphodiester bond hydrolysis, endonucleolytic Source: GOC
  • rRNA catabolic process Source: InterPro
  • rRNA processing Source: SGD
  • rRNA transcription Source: SGD
  • termination of RNA polymerase II transcription, exosome-dependent Source: SGD
  • U1 snRNA 3'-end processing Source: SGD
  • U4 snRNA 3'-end processing Source: SGD
  • U5 snRNA 3'-end processing Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:YMR239C-MONOMER.
BRENDAi3.1.26.3. 984.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease 3 (EC:3.1.26.3)
Alternative name(s):
Ribonuclease III
Short name:
RNase III
Gene namesi
Name:RNT1
Ordered Locus Names:YMR239C
ORF Names:YM9408.01C, YM9959.21
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XIII

Organism-specific databases

CYGDiYMR239c.
EuPathDBiFungiDB:YMR239C.
SGDiS000004852. RNT1.

Subcellular locationi

GO - Cellular componenti

  • nucleolus Source: SGD
  • nucleoplasm Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 471471Ribonuclease 3PRO_0000180466Add
BLAST

Proteomic databases

MaxQBiQ02555.
PaxDbiQ02555.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
SEN1Q004162EBI-15673,EBI-16945

Protein-protein interaction databases

BioGridi35418. 50 interactions.
DIPiDIP-4298N.
IntActiQ02555. 8 interactions.
MINTiMINT-567072.
STRINGi4932.YMR239C.

Structurei

Secondary structure

1
471
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi46 – 6924Combined sources
Helixi73 – 819Combined sources
Beta strandi84 – 863Combined sources
Helixi88 – 958Combined sources
Helixi97 – 11014Combined sources
Helixi116 – 12611Combined sources
Beta strandi136 – 1383Combined sources
Helixi140 – 14910Combined sources
Helixi208 – 2136Combined sources
Helixi218 – 2214Combined sources
Helixi229 – 2335Combined sources
Helixi238 – 25922Combined sources
Helixi265 – 27612Combined sources
Helixi278 – 28710Combined sources
Helixi290 – 2934Combined sources
Turni306 – 3094Combined sources
Helixi313 – 32917Combined sources
Helixi331 – 35626Combined sources
Helixi358 – 3603Combined sources
Helixi370 – 3789Combined sources
Helixi381 – 3833Combined sources
Beta strandi386 – 3916Combined sources
Beta strandi394 – 3963Combined sources
Beta strandi400 – 4056Combined sources
Turni407 – 4093Combined sources
Beta strandi411 – 4199Combined sources
Helixi420 – 43314Combined sources
Helixi435 – 4417Combined sources
Helixi450 – 4534Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1T4LNMR-B366-453[»]
1T4NNMR-A364-447[»]
1T4OX-ray2.50A/B362-471[»]
2LBSNMR-B366-453[»]
2LUPNMR-B366-453[»]
2LUQNMR-A366-453[»]
4OOGX-ray2.50A/B42-151[»]
C197-457[»]
ProteinModelPortaliQ02555.
SMRiQ02555. Positions 42-151, 197-457.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ02555.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini227 – 331105RNase IIIPROSITE-ProRule annotationAdd
BLAST
Domaini369 – 43769DRBMPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 DRBM (double-stranded RNA-binding) domain.PROSITE-ProRule annotation
Contains 1 RNase III domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0571.
HOGENOMiHOG000000766.
InParanoidiQ02555.
KOiK03685.
OMAiMIIYNKF.
OrthoDBiEOG7M0P26.

Family and domain databases

Gene3Di1.10.1520.10. 1 hit.
3.30.160.20. 1 hit.
InterProiIPR014720. dsRNA-bd_dom.
IPR000999. RNase_III_dom.
[Graphical view]
PfamiPF00035. dsrm. 1 hit.
PF00636. Ribonuclease_3. 1 hit.
[Graphical view]
SMARTiSM00358. DSRM. 1 hit.
SM00535. RIBOc. 1 hit.
[Graphical view]
SUPFAMiSSF69065. SSF69065. 1 hit.
PROSITEiPS50137. DS_RBD. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q02555-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGSKVAGKKK TQNDNKLDNE NGSQQRENIN TKTLLKGNLK ISNYKYLEVI
60 70 80 90 100
QLEHAVTKLV ESYNKIIELS PNLVAYNEAV NNQDRVPVQI LPSLSRYQLK
110 120 130 140 150
LAAELKTLHD LKKDAILTEI TDYENEFDTE QKQPILQEIS KADMEKLEKL
160 170 180 190 200
EQVKREKREK IDVNVYENLN EKEDEEEDEG EDSYDPTKAG DIVKATKWPP
210 220 230 240 250
KLPEIQDLAI RARVFIHKST IKDKVYLSGS EMINAHNERL EFLGDSILNS
260 270 280 290 300
VMTLIIYNKF PDYSEGQLST LRMNLVSNEQ IKQWSIMYNF HEKLKTNFDL
310 320 330 340 350
KDENSNFQNG KLKLYADVFE AYIGGLMEDD PRNNLPKIRK WLRKLAKPVI
360 370 380 390 400
EEATRNQVAL EKTDKLDMNA KRQLYSLIGY ASLRLHYVTV KKPTAVDPNS
410 420 430 440 450
IVECRVGDGT VLGTGVGRNI KIAGIRAAEN ALRDKKMLDF YAKQRAAIPR
460 470
SESVLKDPSQ KNKKRKFSDT S
Length:471
Mass (Da):54,071
Last modified:November 1, 1997 - v1
Checksum:i570294172E66A0DE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U27016 Genomic DNA. Translation: AAB04172.1.
Z48756 Genomic DNA. Translation: CAA88649.1.
Z49939 Genomic DNA. Translation: CAA90210.1.
BK006946 Genomic DNA. Translation: DAA10139.1.
PIRiS56053.
RefSeqiNP_013966.1. NM_001182746.1.

Genome annotation databases

EnsemblFungiiYMR239C; YMR239C; YMR239C.
GeneIDi855280.
KEGGisce:YMR239C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U27016 Genomic DNA. Translation: AAB04172.1.
Z48756 Genomic DNA. Translation: CAA88649.1.
Z49939 Genomic DNA. Translation: CAA90210.1.
BK006946 Genomic DNA. Translation: DAA10139.1.
PIRiS56053.
RefSeqiNP_013966.1. NM_001182746.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1T4LNMR-B366-453[»]
1T4NNMR-A364-447[»]
1T4OX-ray2.50A/B362-471[»]
2LBSNMR-B366-453[»]
2LUPNMR-B366-453[»]
2LUQNMR-A366-453[»]
4OOGX-ray2.50A/B42-151[»]
C197-457[»]
ProteinModelPortaliQ02555.
SMRiQ02555. Positions 42-151, 197-457.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35418. 50 interactions.
DIPiDIP-4298N.
IntActiQ02555. 8 interactions.
MINTiMINT-567072.
STRINGi4932.YMR239C.

Proteomic databases

MaxQBiQ02555.
PaxDbiQ02555.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYMR239C; YMR239C; YMR239C.
GeneIDi855280.
KEGGisce:YMR239C.

Organism-specific databases

CYGDiYMR239c.
EuPathDBiFungiDB:YMR239C.
SGDiS000004852. RNT1.

Phylogenomic databases

eggNOGiCOG0571.
HOGENOMiHOG000000766.
InParanoidiQ02555.
KOiK03685.
OMAiMIIYNKF.
OrthoDBiEOG7M0P26.

Enzyme and pathway databases

BioCyciYEAST:YMR239C-MONOMER.
BRENDAi3.1.26.3. 984.

Miscellaneous databases

EvolutionaryTraceiQ02555.
NextBioi978911.
PROiQ02555.

Family and domain databases

Gene3Di1.10.1520.10. 1 hit.
3.30.160.20. 1 hit.
InterProiIPR014720. dsRNA-bd_dom.
IPR000999. RNase_III_dom.
[Graphical view]
PfamiPF00035. dsrm. 1 hit.
PF00636. Ribonuclease_3. 1 hit.
[Graphical view]
SMARTiSM00358. DSRM. 1 hit.
SM00535. RIBOc. 1 hit.
[Graphical view]
SUPFAMiSSF69065. SSF69065. 1 hit.
PROSITEiPS50137. DS_RBD. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site."
    Elela S.A., Igel H., Ares M. Jr.
    Cell 85:115-124(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRNT1_YEAST
AccessioniPrimary (citable) accession number: Q02555
Secondary accession number(s): D6W065, Q04008, Q05038
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: June 24, 2015
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 4970 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

External Data

Dasty 3

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 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.