NUDC_VIBPA
ID NUDC_VIBPA Reviewed; 260 AA.
AC Q87KQ7;
DT 25-JUL-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 96.
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=VP2919;
OS Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=223926;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RIMD 2210633;
RX PubMed=12620739; DOI=10.1016/s0140-6736(03)12659-1;
RA Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K.,
RA Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S.,
RA Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.;
RT "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism
RT distinct from that of V. cholerae.";
RL Lancet 361:743-749(2003).
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; BA000031; BAC61182.1; -; Genomic_DNA.
DR RefSeq; NP_799298.1; NC_004603.1.
DR RefSeq; WP_005456481.1; NC_004603.1.
DR AlphaFoldDB; Q87KQ7; -.
DR SMR; Q87KQ7; -.
DR STRING; 223926.28807945; -.
DR EnsemblBacteria; BAC61182; BAC61182; BAC61182.
DR GeneID; 1190494; -.
DR KEGG; vpa:VP2919; -.
DR PATRIC; fig|223926.6.peg.2807; -.
DR eggNOG; COG2816; Bacteria.
DR HOGENOM; CLU_037162_0_1_6; -.
DR OMA; TWAREHR; -.
DR Proteomes; UP000002493; 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; 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 SUPFAM; SSF55811; SSF55811; 1.
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..260
FT /note="NAD-capped RNA hydrolase NudC"
FT /id="PRO_0000056979"
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 260 AA; 29296 MW; 5659643CBF890E7E CRC64;
MLRKGDVNRV ANAYWCVVAG SEIWLVDGAV PFGSAEQFSL PEENARQIGD YLGSPVMWIN
FADLEQDLPL VSLRDCLHFP EPLFMLLSKA IQYGHMTQSL RFCPQCGGRN FLNNNQFAMQ
CGECRTLHYP RIFPCIIVAV RKENQILLAQ HPRHRNGMYT VIAGFLEAGE TLEDCVAREV
HEETGIHVKN IRYFGSQPWA FPSSMMMAFL ADYDSGELNP DYTELSDAQW FGVKEMPPVA
PTGTIARALI EQTISDILSD
