ID A0A385Z435_9PSED Unreviewed; 277 AA.
AC A0A385Z435;
DT 05-DEC-2018, integrated into UniProtKB/TrEMBL.
DT 05-DEC-2018, sequence version 1.
DT 27-MAR-2024, entry version 20.
DE RecName: Full=NAD-capped RNA hydrolase NudC {ECO:0000256|HAMAP-Rule:MF_00297};
DE Short=DeNADding enzyme NudC {ECO:0000256|HAMAP-Rule:MF_00297};
DE EC=3.6.1.- {ECO:0000256|HAMAP-Rule:MF_00297};
DE AltName: Full=NADH pyrophosphatase {ECO:0000256|HAMAP-Rule:MF_00297};
DE EC=3.6.1.22 {ECO:0000256|HAMAP-Rule:MF_00297};
GN Name=nudC {ECO:0000256|HAMAP-Rule:MF_00297};
GN ORFNames=D3880_10945 {ECO:0000313|EMBL:AYC32857.1};
OS Pseudomonas cavernae.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=2320867 {ECO:0000313|EMBL:AYC32857.1, ECO:0000313|Proteomes:UP000265560};
RN [1] {ECO:0000313|Proteomes:UP000265560}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K2W31S-8 {ECO:0000313|Proteomes:UP000265560};
RA Zhu H.;
RL Submitted (SEP-2018) 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:0000256|HAMAP-
CC 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:0000256|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:0000256|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:0000256|ARBA:ARBA00023679};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60877;
CC Evidence={ECO:0000256|ARBA:ARBA00023679};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00297};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00297};
CC Note=Divalent metal cations. Mg(2+) or Mn(2+). {ECO:0000256|HAMAP-
CC Rule:MF_00297};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00297};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000256|HAMAP-Rule:MF_00297};
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00297}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NudC subfamily.
CC {ECO:0000256|ARBA:ARBA00009595, ECO:0000256|HAMAP-Rule:MF_00297}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00297}.
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DR EMBL; CP032419; AYC32857.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A385Z435; -.
DR KEGG; pcav:D3880_10945; -.
DR OrthoDB; 9791656at2; -.
DR Proteomes; UP000265560; Chromosome.
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; 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 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 PRINTS; PR00502; NUDIXFAMILY.
DR SUPFAM; SSF55811; Nudix; 2.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 3: Inferred from homology;
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_00297};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00297};
KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|HAMAP-Rule:MF_00297};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00297};
KW NAD {ECO:0000256|ARBA:ARBA00023027, ECO:0000256|HAMAP-Rule:MF_00297};
KW Reference proteome {ECO:0000313|Proteomes:UP000265560};
KW Zinc {ECO:0000256|HAMAP-Rule:MF_00297}.
FT DOMAIN 140..263
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000259|PROSITE:PS51462"
FT MOTIF 174..195
FT /note="Nudix box"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 83
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 113
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 116
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 126
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 131
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 134
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 139
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 173
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 189
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 189
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 193
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 193
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 207..214
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 234
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 234
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 256
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
SQ SEQUENCE 277 AA; 31168 MW; 2C7233C3421306FB CRC64;
MEQGWQTTPA LDNSLPGGWA LARCQQGFLA DSNGVLFPRE WLKRQELSLS AEHGLGYFNG
EPVWLLELQQ PAEVMGCHWQ GLRQFMLQAD YPTFRMLSFA EQIGSWSSQH RFCGRCGSPT
RQVPGERCMR CPGCGLDSYA RISPSMIVLV TRGDEILLAR SPRFVPGMYS TLAGFVEPGE
SVEECVAREV REEVGLEVGN LQYLGSQGWP FPHSLMLGFH AEYAAGDITP QADEIEDARW
FPIEQLPPLP MQRSIARYLI DLYLARRLGH PEPVLPR
//