P53164 · NPY1_YEAST
- ProteinNAD-capped RNA hydrolase NPY1
- GeneNPY1
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids384 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
mRNA decapping enzyme that specifically removes the nicotinamide adenine dinucleotide (NAD) cap from a subset of mRNAs by hydrolyzing the diphosphate linkage to produce nicotinamide mononucleotide (NMN) and 5' monophosphate mRNA. The NAD-cap is present at the 5'-end of some RNAs; in contrast to the canonical N7 methylguanosine (m7G) cap, the NAD cap promotes mRNA decay (By similarity).
Mediates the hydrolysis of some nucleoside diphosphate derivatives (PubMed:11361135).
Mediates the hydrolysis of some nucleoside diphosphate derivatives (PubMed:11361135).
Miscellaneous
Present with 846 molecules/cell in log phase SD medium.
Catalytic activity
- a 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H+This reaction proceeds in the forward direction.
Cofactor
Protein has several cofactor binding sites:
Note: Binds 3 Mg2+ ions per subunit.
Note: Binds 1 zinc ion per subunit.
Kinetics
KM | SUBSTRATE | pH | TEMPERATURE[C] | NOTES | EVIDENCE | |
---|---|---|---|---|---|---|
0.17 mM | NADH | |||||
0.5 mM | NAD+ | |||||
1.3 mM | ADP-ribose |
Vmax | pH | TEMPERATURE[C] | NOTES | EVIDENCE | |
---|---|---|---|---|---|
2 μmol/min/mg | with NADH as substrate | ||||
0.85 μmol/min/mg | with NAD+ as substrate | ||||
0.8 μmol/min/mg | with ADP-ribose as substrate |
kcat is 1.5 sec-1 for NADH. kcat is 0.6 sec-1 for NAD+. kcat is 0.6 sec-1 for ADP-ribose.
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 179 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 182 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 197 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 206 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 256 | Mg2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: A | ||||||
Binding site | 256-258 | substrate | ||||
Sequence: AGF | ||||||
Binding site | 272 | Mg2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 272 | Mg2+ 3 (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 272 | substrate | ||||
Sequence: E | ||||||
Binding site | 276 | Mg2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 276 | Mg2+ 3 (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 276 | substrate | ||||
Sequence: E | ||||||
Binding site | 322 | Mg2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 322 | Mg2+ 3 (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 322 | substrate | ||||
Sequence: E |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasm | |
Cellular Component | cytosol | |
Cellular Component | peroxisome | |
Molecular Function | metal ion binding | |
Molecular Function | NAD+ diphosphatase activity | |
Molecular Function | NADH pyrophosphatase activity | |
Molecular Function | RNA NAD-cap (NMN-forming) hydrolase activity | |
Biological Process | NAD catabolic process | |
Biological Process | NAD-cap decapping | |
Biological Process | NADH metabolic process | |
Biological Process | NADP catabolic process | |
Biological Process | RNA decapping |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameNAD-capped RNA hydrolase NPY1
- EC number
- Short namesDeNADding enzyme NPY1
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageEukaryota > Fungi > Dikarya > Ascomycota > Saccharomycotina > Saccharomycetes > Saccharomycetales > Saccharomycetaceae > Saccharomyces
Accessions
- Primary accessionP53164
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000056961 | 1-384 | NAD-capped RNA hydrolase NPY1 | |||
Sequence: MSTAVTFFGQHVLNRVSFLRCSKEFIKKSLNHDSTVFIPFIEGEALISPENGDLVQLSNSVKSYKNILSAIVPLYTTLLNTTRSRSDESGINVTFLGLLEGTDSAFNFEWSNISYKGTPYFGLDIRVTESTLFKKVDFEPIFSYPKVTRDHIFKQTNEDASLYSQGKMYLDWLAKYKFCPGCGSPLFPVEAGTKLQCSNENRNVYCNVRDARINNVCFPRTDPTVIIALTNSDYSKCCLARSKKRYGDFVLYSTIAGFMEPSETIEEACIREIWEETGISCKNIDIVRSQPWPYPCSLMIGCLGIVQFNSKNEVINLNHDDELLDAQWFDTTEIIQALDKYAGGYRVPFKNDINLPGSTTIAFQLINHVCENYKNLRKTSSSHL |
Proteomic databases
Structure
Family & Domains
Features
Showing features for domain, motif.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 219-351 | Nudix hydrolase | ||||
Sequence: PRTDPTVIIALTNSDYSKCCLARSKKRYGDFVLYSTIAGFMEPSETIEEACIREIWEETGISCKNIDIVRSQPWPYPCSLMIGCLGIVQFNSKNEVINLNHDDELLDAQWFDTTEIIQALDKYAGGYRVPFKN | ||||||
Motif | 257-278 | Nudix box | ||||
Sequence: GFMEPSETIEEACIREIWEETG | ||||||
Motif | 378-380 | Microbody targeting signal | ||||
Sequence: KTS |
Sequence similarities
Belongs to the Nudix hydrolase family. NudC subfamily.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length384
- Mass (Da)43,516
- Last updated1996-10-01 v1
- Checksum96D6768CE2BC8F0B
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 44 | in Ref. 3; AAT93207 | ||||
Sequence: E → D |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
Z72589 EMBL· GenBank· DDBJ | CAA96771.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AY693188 EMBL· GenBank· DDBJ | AAT93207.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BK006941 EMBL· GenBank· DDBJ | DAA08035.1 EMBL· GenBank· DDBJ | Genomic DNA |