ID A0A089NB47_9BACL Unreviewed; 282 AA.
AC A0A089NB47;
DT 26-NOV-2014, integrated into UniProtKB/TrEMBL.
DT 26-NOV-2014, sequence version 1.
DT 27-MAR-2024, entry version 44.
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=PSTEL_26210 {ECO:0000313|EMBL:AIQ66089.1};
OS Paenibacillus stellifer.
OC Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus.
OX NCBI_TaxID=169760 {ECO:0000313|EMBL:AIQ66089.1, ECO:0000313|Proteomes:UP000029507};
RN [1] {ECO:0000313|EMBL:AIQ66089.1, ECO:0000313|Proteomes:UP000029507}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14472 {ECO:0000313|EMBL:AIQ66089.1,
RC ECO:0000313|Proteomes:UP000029507};
RA den Bakker H.C., Tsai Y.-C., Martin N., Korlach J., Wiedmann M.;
RT "Comparative genomics of the Paenibacillus odorifer group.";
RL Submitted (AUG-2014) 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; CP009286; AIQ66089.1; -; Genomic_DNA.
DR RefSeq; WP_038701684.1; NZ_CP009286.1.
DR AlphaFoldDB; A0A089NB47; -.
DR STRING; 169760.PSTEL_26210; -.
DR KEGG; pste:PSTEL_26210; -.
DR HOGENOM; CLU_037162_0_1_9; -.
DR OrthoDB; 9787476at2; -.
DR Proteomes; UP000029507; 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:UP000029507};
KW Zinc {ECO:0000256|HAMAP-Rule:MF_00297}.
FT DOMAIN 152..276
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000259|PROSITE:PS51462"
FT MOTIF 186..207
FT /note="Nudix box"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 95
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 125
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 128
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 138
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 143
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 146
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 151
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 185
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 201
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 201
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 205
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 205
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 219..226
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 246
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 246
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 268
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
SQ SEQUENCE 282 AA; 31206 MW; A171BB99BDA7D8A0 CRC64;
MSKPRLSIYN RYVPAVVQET GFEGPAYWFI FRAGQLLVAE DSGAAAVPLA LSPEELTVAS
IRTLYLGTFG SIPCFAAEAS PEATEPPGLL FRPLRSLYEA MDEDLFHLAG KAVQLLAWDE
THLFCGRCGT QTVPSEAEWS RKCPECGLVS YPRIAPAVIT AVLKGDEILL AHAGHFQNNM
YGLIAGFVEP GETLEDCVQR EIMEEVGLKV TNIRYFGSQQ WPFPHSLMVG FLADYESGEI
AVDGEEIVHA DWFRPDSLPV IPAKVSIARK IIDWYIGQYT RC
//