ID A0A2K9LFL0_9GAMM Unreviewed; 272 AA.
AC A0A2K9LFL0;
DT 25-APR-2018, integrated into UniProtKB/TrEMBL.
DT 25-APR-2018, sequence version 1.
DT 27-MAR-2024, entry version 23.
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=Kalk_01385 {ECO:0000313|EMBL:AUM11166.1};
OS Ketobacter alkanivorans.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Ketobacteraceae; Ketobacter.
OX NCBI_TaxID=1917421 {ECO:0000313|EMBL:AUM11166.1, ECO:0000313|Proteomes:UP000235116};
RN [1] {ECO:0000313|Proteomes:UP000235116}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GI5 {ECO:0000313|Proteomes:UP000235116};
RA Kim S.-J., Rhee S.-K.;
RT "Direct submision.";
RL Submitted (AUG-2017) 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|HAMAP-Rule:MF_00297};
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|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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CP022684; AUM11166.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A2K9LFL0; -.
DR KEGG; kak:Kalk_01385; -.
DR OrthoDB; 9791656at2; -.
DR Proteomes; UP000235116; 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; 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; PTHR11383:SF3; NAD(P)H PYROPHOSPHATASE NUDT13, MITOCHONDRIAL; 1.
DR PANTHER; PTHR11383; NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 13; 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 Reference proteome {ECO:0000313|Proteomes:UP000235116};
KW Zinc {ECO:0000256|HAMAP-Rule:MF_00297}.
FT DOMAIN 143..267
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000259|PROSITE:PS51462"
FT MOTIF 177..198
FT /note="Nudix box"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 86
FT /ligand="substrate"
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 119
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 137
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 142
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 176
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 192
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 192
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 196
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 196
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 210..217
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 237
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 237
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
SQ SEQUENCE 272 AA; 30607 MW; E4E3C6600862C71C CRC64;
MDFVPGVIAP DDHEGEAIWF AFHKGRLLMV QDQYGLMVPQ IDRFSLLGIP HRSPHYLGQL
QSSPCYAVTL ECEGPLPPNY MLHDLRRVAM MVDPNLFMIA GKARQVLDWD TNHRFCGRCG
TETVHHDRDR AKLCPSCGHT QYPRISPCII VLVTKGTEIL LARSPNFPQG MFSTLAGFVE
AGETLEMAVH REIQEEVGVR VKNLEYKGSQ PWPFPHSLMI GFHAEYAGGD IILEDDEIEE
AGWWNINDLP SIPPRGSISH ELIAQYLATM ST
//