ID NUDC_PSEPW Reviewed; 276 AA.
AC B1J6H6;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 29-APR-2008, sequence version 1.
DT 27-MAR-2024, entry version 79.
DE RecName: Full=NAD-capped RNA hydrolase NudC {ECO:0000255|HAMAP-Rule:MF_00297};
DE Short=DeNADding enzyme NudC {ECO:0000255|HAMAP-Rule:MF_00297};
DE EC=3.6.1.- {ECO:0000255|HAMAP-Rule:MF_00297};
DE AltName: Full=NADH pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_00297};
DE EC=3.6.1.22 {ECO:0000255|HAMAP-Rule:MF_00297};
GN Name=nudC {ECO:0000255|HAMAP-Rule:MF_00297};
GN OrderedLocusNames=PputW619_1842;
OS Pseudomonas putida (strain W619).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=390235;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=W619;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S.,
RA Shin M., Vergez L., Schmutz J., Larimer F., Land M., Hauser L.,
RA Kyrpides N., Kim E., Taghavi S., Vangronsveld D., van der Lelie D.,
RA Richardson P.;
RT "Complete sequence of Pseudomonas putida W619.";
RL Submitted (FEB-2008) to the EMBL/GenBank/DDBJ databases.
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 mRNAs and stabilizes RNA against 5'-processing.
CC Has preference for mRNAs with a 5'-end purine. Catalyzes the hydrolysis
CC of a broad range of dinucleotide pyrophosphates. {ECO:0000255|HAMAP-
CC Rule:MF_00297}.
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:0000255|HAMAP-Rule:MF_00297};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60877;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00297};
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:0000255|HAMAP-Rule:MF_00297};
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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00297};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00297};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00297};
CC Note=Divalent metal cations. Mg(2+) or Mn(2+). {ECO:0000255|HAMAP-
CC Rule:MF_00297};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00297};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00297};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00297}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NudC subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00297}.
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DR EMBL; CP000949; ACA72345.1; -; Genomic_DNA.
DR AlphaFoldDB; B1J6H6; -.
DR SMR; B1J6H6; -.
DR STRING; 390235.PputW619_1842; -.
DR KEGG; ppw:PputW619_1842; -.
DR eggNOG; COG2816; Bacteria.
DR HOGENOM; CLU_037162_0_1_6; -.
DR OrthoDB; 9791656at2; -.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000210; F:NAD+ diphosphatase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0035529; F:NADH pyrophosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0110153; F:RNA NAD-cap (NMN-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR CDD; cd03429; NADH_pyrophosphatase; 1.
DR Gene3D; 3.90.79.20; -; 1.
DR Gene3D; 3.90.79.10; Nucleoside Triphosphate Pyrophosphohydrolase; 1.
DR HAMAP; MF_00297; Nudix_NudC; 1.
DR InterPro; IPR015375; NADH_PPase-like_N.
DR InterPro; IPR049734; NudC-like_C.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR InterPro; IPR022925; RNA_Hydrolase_NudC.
DR InterPro; IPR015376; Znr_NADH_PPase.
DR PANTHER; PTHR42904:SF6; NAD-CAPPED RNA HYDROLASE NUDT12; 1.
DR PANTHER; PTHR42904; NUDIX HYDROLASE, NUDC SUBFAMILY; 1.
DR Pfam; PF00293; NUDIX; 1.
DR Pfam; PF09296; NUDIX-like; 1.
DR Pfam; PF09297; zf-NADH-PPase; 1.
DR SUPFAM; SSF55811; Nudix; 2.
DR PROSITE; PS51462; NUDIX; 1.
PE 3: Inferred from homology;
KW Hydrolase; Magnesium; Manganese; Metal-binding; NAD; Zinc.
FT CHAIN 1..276
FT /note="NAD-capped RNA hydrolase NudC"
FT /id="PRO_1000115245"
FT DOMAIN 139..262
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT MOTIF 173..194
FT /note="Nudix box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 82
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 112
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 115
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 125
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 130
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 133
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 138
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 172
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 188
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 188
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 192
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 192
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 206..213
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 233
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 233
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 255
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
SQ SEQUENCE 276 AA; 30963 MW; 37A25BD1C926C66A CRC64;
MSARWTSAVL DPQITGGWAV ARSPEGFLVD ANGALFPRDW LKRQDLDVLA EHGIGHFDGE
PVFLLELRST AEVPGCGWRG LRSFMLEGDF DLYKVLGYAA QIGTWAREHR FCGSCGQPMT
QIRWERAMYC QPCDLRSYPR ISPSMIVLVT RGDEILLARS PRFVTGVYST LAGFAEPGES
AEDCLVREVR EEVAVEVTNI QYVGSQCWPF PHSMMLGFHA EYAGGEIVMQ PDEIEDARWF
NVHDLPPLPA GRSIARYLID LYVARRSGLP EPVLPR
//
