ID J7IYX5_DESMD Unreviewed; 267 AA.
AC J7IYX5;
DT 31-OCT-2012, integrated into UniProtKB/TrEMBL.
DT 31-OCT-2012, sequence version 1.
DT 27-MAR-2024, entry version 58.
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 OrderedLocusNames=Desmer_1944 {ECO:0000313|EMBL:AFQ43896.1};
OS Desulfosporosinus meridiei (strain ATCC BAA-275 / DSM 13257 / KCTC 12902 /
OS NCIMB 13706 / S10).
OC Bacteria; Bacillota; Clostridia; Eubacteriales; Desulfitobacteriaceae;
OC Desulfosporosinus.
OX NCBI_TaxID=768704 {ECO:0000313|EMBL:AFQ43896.1, ECO:0000313|Proteomes:UP000005262};
RN [1] {ECO:0000313|EMBL:AFQ43896.1, ECO:0000313|Proteomes:UP000005262}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-275 / DSM 13257 / NCIMB 13706 / S10
RC {ECO:0000313|Proteomes:UP000005262};
RX PubMed=23105050; DOI=10.1128/JB.01392-12;
RA Pester M., Brambilla E., Alazard D., Rattei T., Weinmaier T., Han J.,
RA Lucas S., Lapidus A., Cheng J.F., Goodwin L., Pitluck S., Peters L.,
RA Ovchinnikova G., Teshima H., Detter J.C., Han C.S., Tapia R., Land M.L.,
RA Hauser L., Kyrpides N.C., Ivanova N.N., Pagani I., Huntmann M., Wei C.L.,
RA Davenport K.W., Daligault H., Chain P.S., Chen A., Mavromatis K.,
RA Markowitz V., Szeto E., Mikhailova N., Pati A., Wagner M., Woyke T.,
RA Ollivier B., Klenk H.P., Spring S., Loy A.;
RT "Complete genome sequences of Desulfosporosinus orientis DSM765T,
RT Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T,
RT and Desulfosporosinus acidiphilus DSM22704T.";
RL J. Bacteriol. 194:6300-6301(2012).
RN [2] {ECO:0000313|Proteomes:UP000005262}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-275 / DSM 13257 / NCIMB 13706 / S10
RC {ECO:0000313|Proteomes:UP000005262};
RA Huntemann M., Wei C.-L., Han J., Detter J.C., Han C., Davenport K.,
RA Daligault H., Erkkila T., Gu W., Munk A.C.C., Teshima H., Xu Y., Chain P.,
RA Tapia R., Chen A., Krypides N., Mavromatis K., Markowitz V., Szeto E.,
RA Ivanova N., Mikhailova N., Ovchinnikova G., Pagani I., Pati A., Goodwin L.,
RA Peters L., Pitluck S., Woyke T., Pester M., Spring S., Ollivier B.,
RA Rattei T., Klenk H.-P., Wagner M., Loy A.;
RT "Finished genome of Desulfosporosinus meridiei DSM 13257.";
RL Submitted (AUG-2012) 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; CP003629; AFQ43896.1; -; Genomic_DNA.
DR RefSeq; WP_014902810.1; NC_018515.1.
DR AlphaFoldDB; J7IYX5; -.
DR STRING; 768704.Desmer_1944; -.
DR KEGG; dmi:Desmer_1944; -.
DR eggNOG; COG2816; Bacteria.
DR HOGENOM; CLU_037162_0_1_9; -.
DR OrthoDB; 9787476at2; -.
DR Proteomes; UP000005262; 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 Zinc {ECO:0000256|HAMAP-Rule:MF_00297}.
FT DOMAIN 137..262
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000259|PROSITE:PS51462"
FT MOTIF 171..192
FT /note="Nudix box"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 110
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
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 123
FT /ligand="substrate"
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 131
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 136
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 170
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 186
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 186
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 190
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 190
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 204..211
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
FT BINDING 231
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 231
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 253
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00297"
SQ SEQUENCE 267 AA; 30374 MW; F7B1295159344B63 CRC64;
MLSKIDGDST AYWLLFKGNK ILISEDKVLE FTLPEIDYFK LSKKLVRSQL LGQMEGRSYY
AAELAPDIVA PETMLFCNLY RLFGKIPDAL FFLAGKAYQI LHWDRTHQYC SQCGARTENK
IDERAKLCPA CGRVNYPRIS PAIIVAITRE REILLARGSR FQADFYSVLA GFVEPGETFE
ECVQREVREE VGLEVKNIRY FGSQPWPFPD SLMVGFTAEY AGGDIKIDEN EILNAGWFDV
DQLPLIPGTG SIARSLIDWF IELAKNE
//
