UniProtKB - P53063 (DXO_YEAST)
Protein
Decapping nuclease RAI1
Gene
RAI1
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Functioni
Decapping enzyme for NAD-capped RNAs: specifically hydrolyzes the nicotinamide adenine dinucleotide (NAD) cap from a subset of RNAs by removing the entire NAD moiety from the 5'-end of an NAD-capped RNA (By similarity). The NAD-cap is present at the 5'-end of some RNAs and snoRNAs. In contrast to the canonical 5'-end N7 methylguanosine (m7G) cap, the NAD cap promotes mRNA decay (By similarity). Also acts as a non-canonical decapping enzyme that removes the entire cap structure of m7G capped or incompletely capped RNAs (PubMed:12897126, PubMed:20802481, PubMed:26101253). Has decapping activity toward incomplete 5'-end m7G cap mRNAs such as unmethylated 5'-end-capped RNA (cap0), while it has no activity toward 2'-O-ribose methylated m7G cap (cap1) (PubMed:12897126, PubMed:20802481). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5'-end triphosphate to release pyrophosphates (PubMed:20802481). Stimulates exoribonuclease activity of RAT1, allowing it to degrade RNAs with stable secondary structure more effectively (PubMed:20802481). Required for the processing of nuclear mRNA and rRNA precursors (PubMed:10805743, PubMed:12612077, PubMed:16131592). May promote termination of transcription by RNA polymerase II (PubMed:15565157).By similarity7 Publications
Miscellaneous
Present with 4030 molecules/cell in log phase SD medium.1 Publication
Catalytic activityi
- a 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-ribonucleoside in mRNA + H+ + NAD+By similarityThis reaction proceeds in the forwardBy similarity direction.
- a 5'-end (N7-methyl 5'-triphosphoguanosine)-adenosine-phospho-ribonucleoside in mRNA + H2O = (N7-methyl 5'-triphospho-guanosine)-adenosine + a 5'-end phospho-ribonucleoside in mRNA + H+1 PublicationThis reaction proceeds in the forward1 Publication direction.
- a 5'-end (N7-methyl 5'-triphosphoguanosine)-guanosine-phospho-ribonucleoside in mRNA + H2O = (N7-methyl 5'-triphospho-guanosine)-guanosine + a 5'-end phospho-ribonucleoside in mRNA + H+1 PublicationThis reaction proceeds in the forward1 Publication direction.
Cofactori
a divalent metal cationBy similarityNote: Divalent metal cation.By similarity
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 172 | Divalent metal cationBy similarity | 1 | |
Binding sitei | 221 | Substrate; via amide nitrogenBy similarity | 1 | |
Metal bindingi | 223 | Divalent metal cationBy similarity | 1 | |
Metal bindingi | 241 | Divalent metal cationBy similarity | 1 | |
Metal bindingi | 242 | Divalent metal cation; via carbonyl oxygenBy similarity | 1 | |
Binding sitei | 243 | SubstrateBy similarity | 1 | |
Binding sitei | 267 | SubstrateBy similarity | 1 |
GO - Molecular functioni
- enzyme regulator activity Source: SGD
- metal ion binding Source: UniProtKB-KW
- nucleotide binding Source: UniProtKB-KW
- phosphodiesterase decapping endonuclease activity Source: SGD
- RNA binding Source: UniProtKB-KW
- RNA pyrophosphohydrolase activity Source: SGD
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
- deadenylation-independent decapping of nuclear-transcribed mRNA Source: SGD
- maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
- maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
- mRNA processing Source: UniProtKB-KW
- NAD-cap decapping Source: GO_Central
- nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
- nuclear-transcribed mRNA catabolic process Source: SGD
- nucleic acid phosphodiester bond hydrolysis Source: GO_Central
- termination of RNA polymerase II transcription, poly(A)-coupled Source: SGD
Keywordsi
Molecular function | Hydrolase, Nuclease, RNA-binding |
Biological process | mRNA processing, rRNA processing, Transcription, Transcription regulation, Transcription termination |
Ligand | Metal-binding, Nucleotide-binding |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:RAI11 Publication Ordered Locus Names:YGL246C ORF Names:NRE387 |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000003215, RAI1 |
VEuPathDBi | FungiDB:YGL246C |
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 221 | E → A: Abolishes the decapping activity. 1 Publication | 1 | |
Mutagenesisi | 223 | D → A: Abolishes the decapping activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | Removed1 Publication | |||
ChainiPRO_0000202708 | 2 – 387 | Decapping nuclease RAI1Add BLAST | 386 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 198 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
PhosphoproteinProteomic databases
MaxQBi | P53063 |
PaxDbi | P53063 |
PRIDEi | P53063 |
PTM databases
iPTMneti | P53063 |
Interactioni
Subunit structurei
Interacts with RAT1, RTT103 and pre-60S ribosomal subunits.
4 PublicationsBinary interactionsi
P53063
With | #Exp. | IntAct |
---|---|---|
RAT1 [Q02792] | 4 | EBI-24206,EBI-14845 |
Protein-protein interaction databases
BioGRIDi | 33033, 75 interactors |
ComplexPortali | CPX-1332, RAT1-RAI1 RNA polymerase II termination complex |
DIPi | DIP-6807N |
IntActi | P53063, 13 interactors |
MINTi | P53063 |
STRINGi | 4932.YGL246C |
Miscellaneous databases
RNActi | P53063, protein |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 273 – 387 | Interaction with RAT1Add BLAST | 115 |
Sequence similaritiesi
Belongs to the DXO/Dom3Z family.Curated
Phylogenomic databases
eggNOGi | KOG1982, Eukaryota |
GeneTreei | ENSGT00390000006425 |
HOGENOMi | CLU_024877_4_1_1 |
InParanoidi | P53063 |
OMAi | YETREGW |
Family and domain databases
InterProi | View protein in InterPro IPR013961, RAI1 IPR039039, RAI1-like_fam |
PANTHERi | PTHR12395, PTHR12395, 1 hit |
Pfami | View protein in Pfam PF08652, RAI1, 1 hit |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
P53063-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MGVSANLFVK QRGSTTALKQ PKEIGFYSRT KDEEYLISDD TNLNYYYLPD
60 70 80 90 100
AELDRKLDLS SGFQKFKDYY KDFEDRCSLR GLLETIESSE RHKGKKINAD
110 120 130 140 150
IITFRGIARK LISCAFDSPS FNTVDLRIVS FNGQLFIKEV PEAVNAAKAS
160 170 180 190 200
SATEAGRNIN QDLNVFTGYK FETLATLSNP LQYTPREVIE KRTKRIVSHG
210 220 230 240 250
DEYISVVRTG VGNCKLILGA EVDCIFDFKE NGRDNLKHYA ELKCTQQVAN
260 270 280 290 300
ISDTHKFERK LFRTWLQCFL VGIPRIIYGF KDDHYVLKTV EEFSTEEVPV
310 320 330 340 350
LLKNNNPQVG SACLEAIKWY GLLTEWLLKM IPRDEDPHSQ IRAFKLVFEN
360 370 380
NHLRLSEIEE SDEEYSGLID GEHILSNGFK EWRKSLK
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 8 | F → S AA sequence (PubMed:10805743).Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X94357 Genomic DNA Translation: CAA64141.1 Z72768 Genomic DNA Translation: CAA96966.1 AY693165 Genomic DNA Translation: AAT93184.1 BK006941 Genomic DNA Translation: DAA07873.1 |
PIRi | S61615 |
RefSeqi | NP_011268.1, NM_001181112.1 |
Genome annotation databases
EnsemblFungii | YGL246C_mRNA; YGL246C; YGL246C |
GeneIDi | 852646 |
KEGGi | sce:YGL246C |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X94357 Genomic DNA Translation: CAA64141.1 Z72768 Genomic DNA Translation: CAA96966.1 AY693165 Genomic DNA Translation: AAT93184.1 BK006941 Genomic DNA Translation: DAA07873.1 |
PIRi | S61615 |
RefSeqi | NP_011268.1, NM_001181112.1 |
3D structure databases
SMRi | P53063 |
ModBasei | Search... |
Protein-protein interaction databases
BioGRIDi | 33033, 75 interactors |
ComplexPortali | CPX-1332, RAT1-RAI1 RNA polymerase II termination complex |
DIPi | DIP-6807N |
IntActi | P53063, 13 interactors |
MINTi | P53063 |
STRINGi | 4932.YGL246C |
PTM databases
iPTMneti | P53063 |
Proteomic databases
MaxQBi | P53063 |
PaxDbi | P53063 |
PRIDEi | P53063 |
Genome annotation databases
EnsemblFungii | YGL246C_mRNA; YGL246C; YGL246C |
GeneIDi | 852646 |
KEGGi | sce:YGL246C |
Organism-specific databases
SGDi | S000003215, RAI1 |
VEuPathDBi | FungiDB:YGL246C |
Phylogenomic databases
eggNOGi | KOG1982, Eukaryota |
GeneTreei | ENSGT00390000006425 |
HOGENOMi | CLU_024877_4_1_1 |
InParanoidi | P53063 |
OMAi | YETREGW |
Miscellaneous databases
PROi | PR:P53063 |
RNActi | P53063, protein |
Family and domain databases
InterProi | View protein in InterPro IPR013961, RAI1 IPR039039, RAI1-like_fam |
PANTHERi | PTHR12395, PTHR12395, 1 hit |
Pfami | View protein in Pfam PF08652, RAI1, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | DXO_YEAST | |
Accessioni | P53063Primary (citable) accession number: P53063 Secondary accession number(s): D6VV89 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | October 1, 1996 |
Last sequence update: | January 23, 2007 | |
Last modified: | February 10, 2021 | |
This is version 165 of the entry and version 3 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Direct protein sequencing, Reference proteomeDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome VII
Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names - SIMILARITY comments
Index of protein domains and families