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Protein

5'-3' exoribonuclease 2

Gene

RAT1

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

Possesses 5'->3' exoribonuclease activity. Required for the processing of nuclear mRNA, rRNA and small nucleolar RNA (snoRNA) precursors. May promote termination of transcription by RNA polymerase II via the recruitment of 3'-end processing factors to the poly(A) site and by the degradation of nascent RNA downstream of the poly(A) site.16 Publications

Catalytic activityi

Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates.

Cofactori

Mg2+2 Publications, Mn2+2 Publications

Enzyme regulationi

Inhibited by nucleoside 3', 5'-bisphosphates.1 Publication

pH dependencei

Optimum pH is 8.0-8.8.1 Publication

GO - Molecular functioni

  • 5'-3' exoribonuclease activity Source: SGD
  • rRNA binding Source: GO_Central

GO - Biological processi

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • mRNA processing Source: UniProtKB-KW
  • negative regulation of phosphorylation of RNA polymerase II C-terminal domain Source: SGD
  • negative regulation of transcription elongation from RNA polymerase II promoter Source: SGD
  • nuclear mRNA surveillance Source: SGD
  • nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
  • rRNA processing Source: SGD
  • snoRNA processing Source: SGD
  • termination of RNA polymerase II transcription, exosome-dependent Source: SGD
  • termination of RNA polymerase II transcription, poly(A)-coupled Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing, rRNA processing, Transcription, Transcription regulation, Transcription termination

Enzyme and pathway databases

BioCyciYEAST:G3O-33592-MONOMER.
ReactomeiR-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
5'-3' exoribonuclease 2 (EC:3.1.13.-)
Alternative name(s):
Ribonucleic acid-trafficking protein 1
p116
Gene namesi
Name:RAT1
Synonyms:HKE1, TAP1
Ordered Locus Names:YOR048C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR048C.
SGDiS000005574. RAT1.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi235D → A: Abrogates exonuclease activity and impairs termination of transcription by RNA polymerase II. 1 Publication1
Mutagenesisi518H → Y: Causes mislocalization to the cytoplasm and suppresses the requirement for XRN1 function. 1 Publication1
Mutagenesisi520L → P: Suppresses the requirement for XRN1 function. 1 Publication1
Mutagenesisi534K → A: Causes mislocalization to the cytoplasm; when associated with A-535 and A-537. 1 Publication1
Mutagenesisi535K → A: Causes mislocalization to the cytoplasm; when associated with A-534 and A-537. 1 Publication1
Mutagenesisi535K → N: Causes mislocalization to the cytoplasm and suppresses the requirement for XRN1 function. 1 Publication1
Mutagenesisi537K → A: Causes mislocalization to the cytoplasm; when associated with A-534 and A-535. 1 Publication1
Mutagenesisi537K → E: Causes mislocalization to the cytoplasm and suppresses the requirement for XRN1 function. 1 Publication1
Mutagenesisi683Y → H in allele TAP1-1; activates transcription of the promoter-defective yeast SUP4 tRNA(Tyr) allele SUP4A53T61. 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000713992 – 10065'-3' exoribonuclease 2Add BLAST1005

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei574PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ02792.
PRIDEiQ02792.

PTM databases

iPTMnetiQ02792.

Interactioni

Subunit structurei

Interacts with RAI1 and RTT103.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RAI1P530635EBI-14845,EBI-24206

Protein-protein interaction databases

BioGridi34449. 57 interactors.
DIPiDIP-6692N.
IntActiQ02792. 4 interactors.
MINTiMINT-639904.

Structurei

3D structure databases

ProteinModelPortaliQ02792.
SMRiQ02792.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati955 – 9581-14
Repeati961 – 9642-14
Repeati972 – 9752-24
Repeati975 – 9783-14
Repeati984 – 9863-23
Repeati996 – 9991-24

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni492 – 529Required for retention in the nucleusAdd BLAST38
Regioni955 – 9992 X 4 AA repeats of S-R-Y-D, N-N-N-Y, Y-S-G-NAdd BLAST45

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili256 – 287Sequence analysisAdd BLAST32
Coiled coili453 – 544Sequence analysisAdd BLAST92

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi933 – 1004Asn-richAdd BLAST72

Sequence similaritiesi

Keywords - Domaini

Coiled coil, Repeat

Phylogenomic databases

GeneTreeiENSGT00670000098098.
HOGENOMiHOG000205514.
KOiK12619.
OMAiPTWRKLM.
OrthoDBiEOG092C068M.

Family and domain databases

InterProiIPR027073. 5_3_exoribonuclease.
IPR017151. 5_3_exoribonuclease_2/3.
IPR004859. Put_53exo.
[Graphical view]
PANTHERiPTHR12341. PTHR12341. 3 hits.
PfamiPF03159. XRN_N. 1 hit.
[Graphical view]
PIRSFiPIRSF037239. Exonuclease_Xrn2. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q02792-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGVPSFFRWL SRKYPKIISP VLEEQPQIVD GVILPLDYSA SNPNGELDNL
60 70 80 90 100
YLDMNGIVHP CSHPENKPPP ETEDEMLLAV FEYTNRVLNM ARPRKVLVMA
110 120 130 140 150
VDGVAPRAKM NQQRARRFRS ARDAQIENEA REEIMRQREE VGEIIDDAVR
160 170 180 190 200
NKKTWDSNAI TPGTPFMDKL AAALRYWTAF KLATDPGWKN LQVIISDATV
210 220 230 240 250
PGEGEHKIMN FIRSQRADPE YNPNTTHCIY GLDADLIFLG LATHEPHFKI
260 270 280 290 300
LREDVFAQDN RKRNNLKDTI NMTEEEKQFL QKQNSEQPFL WLHINVLREY
310 320 330 340 350
LSAELWVPGL PFTFDLERAI DDWVFMCFFC GNDFLPHLPC LDVRENSIDI
360 370 380 390 400
LLDIWKVVLP KLKTYMTCDG VLNLPSVETL LQHLGSREGD IFKTRHIQEA
410 420 430 440 450
RKKEAFERRK AQKNMSKGQD RHPTVATEQL QMYDTQGNLA KGSWNLTTSD
460 470 480 490 500
MVRLKKELML ANEGNEEAIA KVKQQSDKNN ELMKDISKEE IDDAVSKANK
510 520 530 540 550
TNFNLAEVMK QKIINKKHRL EKDNEEEEIA KDSKKVKTEK AESECDLDAE
560 570 580 590 600
IKDEIVADVN DRENSETTEV SRDSPVHSTV NVSEGPKNGV FDTDEFVKLF
610 620 630 640 650
EPGYHERYYT AKFHVTPQDI EQLRKDMVKC YIEGVAWVLM YYYQGCASWN
660 670 680 690 700
WFYPYHYAPL ATDFHGFSHL EIKFEEGTPF LPYEQLMSVL PAASGHALPK
710 720 730 740 750
IFRSLMSEPD SEIIDFYPEE FPIDMNGKKM SWQGIALLPF IDQDRLLTAV
760 770 780 790 800
RAQYPLLSDA ERARNIRGEP VLLISNKNAN YERFSKKLYS KENNNNNVVV
810 820 830 840 850
KFQHFKSGLS GIVSKDVEGF ELNGKIVCPI QGGSLPNLST TLILKMSYRL
860 870 880 890 900
IPLPSRNKSI ILNGFIPSEP VLTAYDLDSI MYKYNNQNYS RRWNFGNDLK
910 920 930 940 950
QNIVPVGPKG ITQYKPRTGG YRAFFYFAEL SRNNVQPAHN YGRNSYNSQP
960 970 980 990 1000
GFNNSRYDGG NNNYRQNSNY RNNNYSGNRN SGQYSGNSYS RNNKQSRYDN

SRANRR
Length:1,006
Mass (Da):115,934
Last modified:January 23, 2007 - v3
Checksum:i5DDD5B0245F3E12A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M95626 Genomic DNA. Translation: AAA34960.1.
Z11746 Genomic DNA. No translation available.
S61567 Genomic DNA. Translation: AAB26818.1.
Z74956 Genomic DNA. Translation: CAA99240.1.
L06011 Unassigned DNA. Translation: AAA16950.1.
BK006948 Genomic DNA. Translation: DAA10830.1.
PIRiS20126.
RefSeqiNP_014691.1. NM_001183467.1.

Genome annotation databases

EnsemblFungiiYOR048C; YOR048C; YOR048C.
GeneIDi854213.
KEGGisce:YOR048C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M95626 Genomic DNA. Translation: AAA34960.1.
Z11746 Genomic DNA. No translation available.
S61567 Genomic DNA. Translation: AAB26818.1.
Z74956 Genomic DNA. Translation: CAA99240.1.
L06011 Unassigned DNA. Translation: AAA16950.1.
BK006948 Genomic DNA. Translation: DAA10830.1.
PIRiS20126.
RefSeqiNP_014691.1. NM_001183467.1.

3D structure databases

ProteinModelPortaliQ02792.
SMRiQ02792.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34449. 57 interactors.
DIPiDIP-6692N.
IntActiQ02792. 4 interactors.
MINTiMINT-639904.

PTM databases

iPTMnetiQ02792.

Proteomic databases

MaxQBiQ02792.
PRIDEiQ02792.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOR048C; YOR048C; YOR048C.
GeneIDi854213.
KEGGisce:YOR048C.

Organism-specific databases

EuPathDBiFungiDB:YOR048C.
SGDiS000005574. RAT1.

Phylogenomic databases

GeneTreeiENSGT00670000098098.
HOGENOMiHOG000205514.
KOiK12619.
OMAiPTWRKLM.
OrthoDBiEOG092C068M.

Enzyme and pathway databases

BioCyciYEAST:G3O-33592-MONOMER.
ReactomeiR-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Miscellaneous databases

PROiQ02792.

Family and domain databases

InterProiIPR027073. 5_3_exoribonuclease.
IPR017151. 5_3_exoribonuclease_2/3.
IPR004859. Put_53exo.
[Graphical view]
PANTHERiPTHR12341. PTHR12341. 3 hits.
PfamiPF03159. XRN_N. 1 hit.
[Graphical view]
PIRSFiPIRSF037239. Exonuclease_Xrn2. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiXRN2_YEAST
AccessioniPrimary (citable) accession number: Q02792
Secondary accession number(s): D6W2B4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 147 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 623 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

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

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.