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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.

Miscellaneous

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

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphomonoester.

GO - Molecular functioni

  • double-stranded RNA binding Source: GO_Central
  • ribonuclease III activity Source: SGD

GO - Biological processi

  • box C/D snoRNA processing Source: SGD
  • box H/ACA snoRNA processing Source: SGD
  • chromatin organization Source: SGD
  • nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay Source: SGD
  • pre-miRNA processing Source: GO_Central
  • primary miRNA processing Source: GO_Central
  • production of siRNA involved in RNA interference Source: GO_Central
  • regulation of fungal-type cell wall organization Source: SGD
  • 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

Keywordsi

Molecular functionEndonuclease, Hydrolase, Nuclease, 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
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR239C.
SGDiS000004852. RNT1.

Subcellular locationi

GO - Cellular componenti

  • nucleolus Source: SGD
  • nucleoplasm Source: SGD

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001804661 – 471Ribonuclease 3Add BLAST471

Proteomic databases

MaxQBiQ02555.
PRIDEiQ02555.

Interactioni

Binary interactionsi

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

Protein-protein interaction databases

BioGridi35418. 324 interactors.
DIPiDIP-4298N.
IntActiQ02555. 8 interactors.
MINTiMINT-567072.
STRINGi4932.YMR239C.

Structurei

Secondary structure

1471
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi46 – 69Combined sources24
Helixi73 – 81Combined sources9
Beta strandi84 – 86Combined sources3
Helixi88 – 95Combined sources8
Helixi97 – 110Combined sources14
Helixi116 – 126Combined sources11
Beta strandi136 – 138Combined sources3
Helixi140 – 149Combined sources10
Helixi208 – 213Combined sources6
Helixi218 – 221Combined sources4
Helixi229 – 233Combined sources5
Helixi238 – 259Combined sources22
Helixi265 – 276Combined sources12
Helixi278 – 287Combined sources10
Helixi290 – 293Combined sources4
Beta strandi303 – 305Combined sources3
Turni306 – 309Combined sources4
Helixi313 – 329Combined sources17
Helixi331 – 356Combined sources26
Helixi358 – 360Combined sources3
Helixi370 – 378Combined sources9
Helixi381 – 383Combined sources3
Beta strandi386 – 391Combined sources6
Beta strandi394 – 396Combined sources3
Beta strandi400 – 405Combined sources6
Turni407 – 409Combined sources3
Beta strandi411 – 419Combined sources9
Helixi420 – 433Combined sources14
Helixi435 – 441Combined sources7
Helixi450 – 453Combined sources4
Beta strandi455 – 457Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5T16X-ray2.78A/B/I/J184-459[»]
C/D/E/F/K/L/M/N41-159[»]
ProteinModelPortaliQ02555.
SMRiQ02555.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ02555.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini227 – 331RNase IIIPROSITE-ProRule annotationAdd BLAST105
Domaini369 – 437DRBMPROSITE-ProRule annotationAdd BLAST69

Phylogenomic databases

HOGENOMiHOG000000766.
InParanoidiQ02555.
KOiK03685.
OMAiARVFIHK.
OrthoDBiEOG092C2YRH.

Family and domain databases

CDDicd00593. RIBOc. 1 hit.
Gene3Di1.10.1520.10. 1 hit.
InterProiView protein in InterPro
IPR014720. dsRBD_dom.
IPR000999. RNase_III_dom.
PfamiView protein in Pfam
PF00035. dsrm. 1 hit.
PF00636. Ribonuclease_3. 1 hit.
SMARTiView protein in SMART
SM00358. DSRM. 1 hit.
SM00535. RIBOc. 1 hit.
SUPFAMiSSF69065. SSF69065. 1 hit.
PROSITEiView protein in PROSITE
PS50137. DS_RBD. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 1 hit.

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.

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.

Entry informationi

Entry nameiRNT1_YEAST
AccessioniPrimary (citable) accession number: Q02555
Secondary accession number(s): D6W065, Q04008, Q05038
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: July 5, 2017
This is version 147 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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