NUDC_PHOPR
ID NUDC_PHOPR Reviewed; 266 AA.
AC Q6LLW5;
DT 26-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 97.
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}; OrderedLocusNames=PBPRA3429;
OS Photobacterium profundum (strain SS9).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Photobacterium.
OX NCBI_TaxID=298386;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1253 / SS9;
RX PubMed=15746425; DOI=10.1126/science.1103341;
RA Vezzi A., Campanaro S., D'Angelo M., Simonato F., Vitulo N., Lauro F.M.,
RA Cestaro A., Malacrida G., Simionati B., Cannata N., Romualdi C.,
RA Bartlett D.H., Valle G.;
RT "Life at depth: Photobacterium profundum genome sequence and expression
RT analysis.";
RL Science 307:1459-1461(2005).
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; CR378674; CAG21713.1; -; Genomic_DNA.
DR AlphaFoldDB; Q6LLW5; -.
DR SMR; Q6LLW5; -.
DR STRING; 298386.PBPRA3429; -.
DR EnsemblBacteria; CAG21713; CAG21713; PBPRA3429.
DR KEGG; ppr:PBPRA3429; -.
DR eggNOG; COG2816; Bacteria.
DR HOGENOM; CLU_037162_0_1_6; -.
DR OMA; TWAREHR; -.
DR Proteomes; UP000000593; Chromosome 1.
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:0110153; F:RNA NAD-cap (NMN-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR HAMAP; MF_00297; Nudix_NudC; 1.
DR InterPro; IPR020476; Nudix_hydrolase.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR InterPro; IPR022925; RNA_Hydrolase_NudC.
DR InterPro; IPR015376; Znr_NADH_PPase.
DR Pfam; PF00293; NUDIX; 1.
DR Pfam; PF09297; zf-NADH-PPase; 1.
DR PRINTS; PR00502; NUDIXFAMILY.
DR SUPFAM; SSF55811; SSF55811; 2.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 3: Inferred from homology;
KW Hydrolase; Magnesium; Manganese; Metal-binding; NAD; Reference proteome;
KW Zinc.
FT CHAIN 1..266
FT /note="NAD-capped RNA hydrolase NudC"
FT /id="PRO_1000071960"
FT DOMAIN 130..253
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT MOTIF 164..185
FT /note="Nudix box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 74
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 106
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 121
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 124
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 129
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 163
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 179
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 179
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 183
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 183
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 197..204
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 224
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 224
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 246
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
SQ SEQUENCE 266 AA; 29872 MW; 7D7FC2212F4AA5F2 CRC64;
MDVILMLNKR ELAYWCVVND RKLYLLDNAI PLLEKSELTF NTDSARVIGE YLDHPVYWLE
ANNCLHSDDF YTQRELLGID QALFDLAGRA TQLSHMLHTQ SFCSVCGGAA VLADDQFAMV
CQQCSNAQYP RVSPCIIVAV RKEDQILLAQ HPRHKTGIYT VIAGFVEAGE TLEQCVAREV
EEETGIQVKN IRYFSSQPWA FPSNIMMAFL ADYESGEINP DYEELSDAIW AKAAELPAIA
PKGTIARVLI DETLALIKAT KHVQNL
