NPY1_CAEEL
ID NPY1_CAEEL Reviewed; 374 AA.
AC Q19427; Q9GPZ5;
DT 11-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 3.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=NAD-capped RNA hydrolase ndx-9 {ECO:0000305};
DE Short=DeNADding enzyme ndx-9 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:Q9DCN1};
DE AltName: Full=NADH pyrophosphatase;
DE EC=3.6.1.22 {ECO:0000269|PubMed:10873676};
DE AltName: Full=Nudix hydrolase 9;
GN Name=ndx-9; ORFNames=F13H10.2;
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 27-374, FUNCTION, CATALYTIC ACTIVITY,
RP COFACTOR, AND SUBUNIT.
RX PubMed=10873676; DOI=10.1006/bbrc.2000.2999;
RA Xu W., Dunn C.A., Bessman M.J.;
RT "Cloning and characterization of the NADH pyrophosphatases from
RT Caenorhabditis elegans and Saccharomyces cerevisiae, members of a Nudix
RT hydrolase subfamily.";
RL Biochem. Biophys. Res. Commun. 273:753-758(2000).
CC -!- FUNCTION: mRNA decapping enzyme that specifically removes the
CC nicotinamide adenine dinucleotide (NAD) cap from a subset of mRNAs by
CC hydrolyzing the diphosphate linkage to produce nicotinamide
CC mononucleotide (NMN) and 5' monophosphate mRNA. The NAD-cap is present
CC at the 5'-end of some RNAs; in contrast to the canonical N7
CC methylguanosine (m7G) cap, the NAD cap promotes mRNA decay (By
CC similarity). Mediates the hydrolysis of some nucleoside diphosphate
CC derivatives (PubMed:10873676). {ECO:0000250|UniProtKB:Q9DCN1,
CC ECO:0000269|PubMed:10873676}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'-
CC end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-
CC nicotinamide D-ribonucleotide + 2 H(+); Xref=Rhea:RHEA:60876,
CC Rhea:RHEA-COMP:15698, Rhea:RHEA-COMP:15719, ChEBI:CHEBI:14649,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:144029,
CC ChEBI:CHEBI:144051; Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60877;
CC Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NAD(+) = AMP + beta-nicotinamide D-ribonucleotide + 2
CC H(+); Xref=Rhea:RHEA:11800, ChEBI:CHEBI:14649, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57540, ChEBI:CHEBI:456215;
CC EC=3.6.1.22; Evidence={ECO:0000269|PubMed:10873676};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NADH = AMP + 2 H(+) + reduced beta-nicotinamide D-
CC ribonucleotide; Xref=Rhea:RHEA:48868, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57945, ChEBI:CHEBI:90832,
CC ChEBI:CHEBI:456215; EC=3.6.1.22;
CC Evidence={ECO:0000269|PubMed:10873676};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:10873676};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:10873676};
CC Note=Divalent metal cations. Binds 3 Mg(2+) or Mn(2+) ions per subunit.
CC {ECO:0000269|PubMed:10873676};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:Q9DCN1};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10873676}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NudC subfamily.
CC {ECO:0000305}.
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DR EMBL; Z68748; CAA92955.3; -; Genomic_DNA.
DR EMBL; AF305937; AAG37064.1; -; mRNA.
DR PIR; T20865; T20865.
DR RefSeq; NP_001129853.1; NM_001136381.2.
DR RefSeq; NP_502051.2; NM_069650.5.
DR AlphaFoldDB; Q19427; -.
DR SMR; Q19427; -.
DR STRING; 6239.F13H10.2a; -.
DR EPD; Q19427; -.
DR PaxDb; Q19427; -.
DR EnsemblMetazoa; F13H10.2a.1; F13H10.2a.1; WBGene00003586.
DR GeneID; 177996; -.
DR KEGG; cel:CELE_F13H10.2; -.
DR UCSC; F13H10.2; c. elegans.
DR CTD; 177996; -.
DR WormBase; F13H10.2a; CE35474; WBGene00003586; ndx-9.
DR eggNOG; KOG3084; Eukaryota.
DR GeneTree; ENSGT00940000157592; -.
DR InParanoid; Q19427; -.
DR OMA; CDMGENV; -.
DR OrthoDB; 1436400at2759; -.
DR PhylomeDB; Q19427; -.
DR Reactome; R-CEL-197264; Nicotinamide salvaging.
DR PRO; PR:Q19427; -.
DR Proteomes; UP000001940; Chromosome IV.
DR Bgee; WBGene00003586; Expressed in germ line (C elegans) and 4 other tissues.
DR ExpressionAtlas; Q19427; baseline and differential.
DR GO; GO:0005777; C:peroxisome; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000210; F:NAD+ diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0035529; F:NADH pyrophosphatase activity; IBA:GO_Central.
DR GO; GO:0110153; F:RNA NAD-cap (NMN-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0019677; P:NAD catabolic process; IBA:GO_Central.
DR GO; GO:0006734; P:NADH metabolic process; IBA:GO_Central.
DR GO; GO:0006742; P:NADP catabolic process; IBA:GO_Central.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Manganese; Metal-binding; NAD; Reference proteome;
KW Zinc.
FT CHAIN 1..374
FT /note="NAD-capped RNA hydrolase ndx-9"
FT /id="PRO_0000056959"
FT DOMAIN 208..336
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 244..265
FT /note="Nudix box"
FT MOTIF 367..369
FT /note="Microbody targeting signal"
FT /evidence="ECO:0000250|UniProtKB:Q9BQG2"
FT BINDING 181
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 184
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 199
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 202
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 207
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 243..245
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 243
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 259
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 259
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 259
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 263
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 263
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 263
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 307
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 307
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 307
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
SQ SEQUENCE 374 AA; 42088 MW; 8195880022A9BFAE CRC64;
MPTFRSNIVV FNLIARRAFT TTSTKNMGFV EKVRLLDYWK IQDSALQSEF PRSRLVLMVD
RRLLVTKDQP DVQMVELSFD DLKQRLGEYG LQFDLSNSCL LDALSTDVDM IPLFGTSIDA
ADPPEDSPIS KKEVLKQLGN SLGGRFTDIR MAMLTMREER QRNLLAKFQS LTKWASIYRR
CPKCAAALKM RSSKSGAECV TCQRVYYPTF SPVSITLITD PTNEHALLVR HRGSAGGVFT
AVAGFAHSGE SMAECARREI AEEVGIEVDS IRSLDMSQPW PMPDSSLMIA HVAVAKIDQK
ISVCPDELET AQWFTRHQVK EALTTTLADP LLKNLPRTLD DRQTLHYIPP AGAIAHQMIR
QWVDGKLENH NSRI
