ID   A0A4T1ZUW9_9PSED        Unreviewed;       275 AA.
AC   A0A4T1ZUW9;
DT   31-JUL-2019, integrated into UniProtKB/TrEMBL.
DT   31-JUL-2019, sequence version 1.
DT   27-MAR-2024, entry version 18.
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=D8779_11205 {ECO:0000313|EMBL:TIH08085.1};
OS   Pseudomonas leptonychotis.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=2448482 {ECO:0000313|EMBL:TIH08085.1, ECO:0000313|Proteomes:UP000307541};
RN   [1] {ECO:0000313|EMBL:TIH08085.1, ECO:0000313|Proteomes:UP000307541}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CCM 8849 {ECO:0000313|EMBL:TIH08085.1,
RC   ECO:0000313|Proteomes:UP000307541};
RA   Novakova D., Svec P., Kralova S., Kristofova L., Zeman M., Pantucek R.,
RA   Maslanova I., Sedlacek I.;
RT   "Pseudomonas leptonychotis sp. nov., isolated from Weddell seals in
RT   Antarctica.";
RL   Submitted (OCT-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}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:TIH08085.1}.
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DR   EMBL; RFLV01000002; TIH08085.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A4T1ZUW9; -.
DR   OrthoDB; 9791656at2; -.
DR   Proteomes; UP000307541; Unassembled WGS sequence.
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; 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   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   Zinc {ECO:0000256|HAMAP-Rule:MF_00297}.
FT   DOMAIN          138..261
FT                   /note="Nudix hydrolase"
FT                   /evidence="ECO:0000259|PROSITE:PS51462"
FT   MOTIF           172..193
FT                   /note="Nudix box"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT   BINDING         81
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT   BINDING         111
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT   BINDING         114
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT   BINDING         124
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT   BINDING         129
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT   BINDING         132
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT   BINDING         137
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT   BINDING         171
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         187
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         187
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         191
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         191
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..212
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT   BINDING         232
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         232
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         254
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
SQ   SEQUENCE   275 AA;  31015 MW;  5051099A42DB561B CRC64;
     MQRWQPTLLD SQLPGGWVVA HFKQHFLADS NGVLFPREWL KQQDLPIVAE HGLGHFDGDA
     IYLLELSQPF DMQGCAWQSL RQFMLQGDAD TFKLLSYATQ IGTWASQHRF CGSCGETMQH
     IPGERAMHCV RCELQHYPRL SPSMIVLVTR GDEVLLARSP RFVSGVYSTL AGFVEAGESV
     EHCVAREVRE EVGVEIKNLQ YLGSQGWPFP HSLMLGFHAE YDSGDIVMQA DEIEDAQWFN
     VHDLPPLPAT RSIARHLIDV YVARRLGHPE PVLPG
//