NUDC_SHIFL
ID NUDC_SHIFL Reviewed; 257 AA.
AC Q83IS3; Q7BZH7;
DT 15-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 117.
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};
GN OrderedLocusNames=SF4068, S3667;
OS Shigella flexneri.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Shigella.
OX NCBI_TaxID=623;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=301 / Serotype 2a;
RX PubMed=12384590; DOI=10.1093/nar/gkf566;
RA Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J.,
RA Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L.,
RA Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H.,
RA Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.;
RT "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT through comparison with genomes of Escherichia coli K12 and O157.";
RL Nucleic Acids Res. 30:4432-4441(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700930 / 2457T / Serotype 2a;
RX PubMed=12704152; DOI=10.1128/iai.71.5.2775-2786.2003;
RA Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G.,
RA Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T.,
RA Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R.;
RT "Complete genome sequence and comparative genomics of Shigella flexneri
RT serotype 2a strain 2457T.";
RL Infect. Immun. 71:2775-2786(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; AE005674; AAN45497.1; -; Genomic_DNA.
DR EMBL; AE014073; AAP18704.1; -; Genomic_DNA.
DR RefSeq; NP_709790.1; NC_004337.2.
DR RefSeq; WP_000373931.1; NZ_WPGW01000040.1.
DR AlphaFoldDB; Q83IS3; -.
DR SMR; Q83IS3; -.
DR STRING; 198214.SF4068; -.
DR EnsemblBacteria; AAN45497; AAN45497; SF4068.
DR EnsemblBacteria; AAP18704; AAP18704; S3667.
DR GeneID; 1025541; -.
DR KEGG; sfl:SF4068; -.
DR KEGG; sfx:S3667; -.
DR PATRIC; fig|198214.7.peg.4792; -.
DR HOGENOM; CLU_037162_0_1_6; -.
DR OMA; TWAREHR; -.
DR OrthoDB; 1435118at2; -.
DR Proteomes; UP000001006; Chromosome.
DR Proteomes; UP000002673; 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: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; 2.
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..257
FT /note="NAD-capped RNA hydrolase NudC"
FT /id="PRO_0000056977"
FT DOMAIN 125..248
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT MOTIF 159..180
FT /note="Nudix box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 25
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 69
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 98
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 111
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 116
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 119
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 124
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 158
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 174
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 174
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 178
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 178
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 192..199
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
FT BINDING 219
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 219
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 241
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00297"
SQ SEQUENCE 257 AA; 29703 MW; 2488D6DD317354C6 CRC64;
MDRIIEKLDH GWWVVSHEQK LWLPKGELPY GEAANFDLVG QRALQIGEWQ GEPVWLIQQQ
RRHDMGSVRQ VIDLDVGLFQ LAGRGVQLAE FYRSHKYCGY CGHEMYPSKT EWAMLCSHCR
ERYYPQIAPC IIVAIRRDDS LLLAQHTRHR NGVHTVLAGF VEVGETLEQA VAREVMEESG
IKVKNLRYVT SQPWPFPQSL MTAFMAEYDS GDIVIDPKEL LEANWYRYDD LPLLPPPGTV
ARRLIEDTVA MCRAEYE
