ADPP_ECOLI
ID ADPP_ECOLI Reviewed; 209 AA.
AC Q93K97; P36651; P82969; Q2M9G6;
DT 13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 13-APR-2004, sequence version 2.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=ADP-ribose pyrophosphatase;
DE EC=3.6.1.13;
DE AltName: Full=ADP-ribose diphosphatase;
DE AltName: Full=ADP-ribose phosphohydrolase;
DE Short=ASPPase;
DE AltName: Full=Adenosine diphosphoribose pyrophosphatase;
DE Short=ADPR-PPase;
GN Name=nudF; Synonyms=aspP, yqiE, yzzG; OrderedLocusNames=b3034, JW3002;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-15, AND FUNCTION.
RC STRAIN=BL21;
RX PubMed=11416161; DOI=10.1073/pnas.131214098;
RA Moreno-Bruna B., Baroja-Fernandez E., Munoz F.J.,
RA Bastarrica-Berasategui A., Zandueta-Criado A., Rodriguez-Lopez M., Lasa I.,
RA Akazawa T., Pozueta-Romero J.;
RT "Adenosine diphosphate sugar pyrophosphatase prevents glycogen biosynthesis
RT in Escherichia coli.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:8128-8132(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 98-209.
RC STRAIN=K12;
RX PubMed=8810311; DOI=10.1074/jbc.271.41.25423;
RA Imamura R., Yamanaka K., Ogura T., Hiraga S., Fujita N., Ishihama A.,
RA Niki H.;
RT "Identification of the cpdA gene encoding cyclic 3',5'-adenosine
RT monophosphate phosphodiesterase in Escherichia coli.";
RL J. Biol. Chem. 271:25423-25429(1996).
RN [5]
RP CHARACTERIZATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=10542272; DOI=10.1074/jbc.274.45.32318;
RA Dunn C.A., O'Handley S.F., Frick D.N., Bessman M.J.;
RT "Studies on the ADP-ribose pyrophosphatase subfamily of the nudix
RT hydrolases and tentative identification of trgB, a gene associated with
RT tellurite resistance.";
RL J. Biol. Chem. 274:32318-32324(1999).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOPROTEIN AND COMPLEXES WITH
RP ADP-RIBOSE AND GADOLINIUM IONS, COFACTOR, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=11323725; DOI=10.1038/87647;
RA Gabelli S.B., Bianchet M.A., Bessman M.J., Amzel L.M.;
RT "The structure of ADP-ribose pyrophosphatase reveals the structural basis
RT for the versatility of the Nudix family.";
RL Nat. Struct. Biol. 8:467-472(2001).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) IN COMPLEX WITH AMPCPR AND MAGNESIUM
RP IONS, COFACTOR, AND CATALYTIC MECHANISM.
RX PubMed=12135348; DOI=10.1021/bi0259296;
RA Gabelli S.B., Bianchet M.A., Ohnishi Y., Ichikawa Y., Bessman M.J.,
RA Amzel L.M.;
RT "Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix
RT hydrolase.";
RL Biochemistry 41:9279-9285(2002).
CC -!- FUNCTION: Acts on ADP-mannose and ADP-glucose as well as ADP-ribose.
CC Prevents glycogen biosynthesis. The reaction catalyzed by this enzyme
CC is a limiting step of the gluconeogenic process.
CC {ECO:0000269|PubMed:11416161}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate + 2 H(+);
CC Xref=Rhea:RHEA:10412, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57967, ChEBI:CHEBI:78346, ChEBI:CHEBI:456215;
CC EC=3.6.1.13; Evidence={ECO:0000269|PubMed:11323725};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11323725, ECO:0000269|PubMed:12135348};
CC Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000269|PubMed:11323725,
CC ECO:0000269|PubMed:12135348};
CC -!- ACTIVITY REGULATION: Inhibited by phosphorylated compounds such as AMP,
CC ADP, ATP, 3-phosphoglyceric acid and PPi. Not inhibited by
CC orthophosphate. Activity is high in cells grown in low glucose
CC concentrations and decreases dramatically as glucose concentration
CC increases.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11323725,
CC ECO:0000269|PubMed:12135348}.
CC -!- INTERACTION:
CC Q93K97; P37678: sgbH; NbExp=2; IntAct=EBI-562814, EBI-555448;
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NudF subfamily.
CC {ECO:0000305}.
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DR EMBL; AJ298136; CAC44036.1; -; Genomic_DNA.
DR EMBL; U28377; AAA69202.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76070.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77090.1; -; Genomic_DNA.
DR EMBL; D16557; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; H65090; H65090.
DR RefSeq; NP_417506.1; NC_000913.3.
DR RefSeq; WP_000917117.1; NZ_STEB01000001.1.
DR PDB; 1G0S; X-ray; 1.90 A; A/B=1-209.
DR PDB; 1G9Q; X-ray; 2.30 A; A/B=1-209.
DR PDB; 1GA7; X-ray; 2.71 A; A/B=1-209.
DR PDB; 1KHZ; X-ray; 2.04 A; A/B=1-209.
DR PDB; 1VIQ; X-ray; 2.40 A; A/B/C=2-209.
DR PDBsum; 1G0S; -.
DR PDBsum; 1G9Q; -.
DR PDBsum; 1GA7; -.
DR PDBsum; 1KHZ; -.
DR PDBsum; 1VIQ; -.
DR AlphaFoldDB; Q93K97; -.
DR SMR; Q93K97; -.
DR BioGRID; 4263247; 23.
DR DIP; DIP-36214N; -.
DR IntAct; Q93K97; 5.
DR STRING; 511145.b3034; -.
DR jPOST; Q93K97; -.
DR PaxDb; Q93K97; -.
DR PRIDE; Q93K97; -.
DR EnsemblBacteria; AAC76070; AAC76070; b3034.
DR EnsemblBacteria; BAE77090; BAE77090; BAE77090.
DR GeneID; 66673067; -.
DR GeneID; 947519; -.
DR KEGG; ecj:JW3002; -.
DR KEGG; eco:b3034; -.
DR PATRIC; fig|1411691.4.peg.3697; -.
DR eggNOG; COG0494; Bacteria.
DR HOGENOM; CLU_062658_6_1_6; -.
DR InParanoid; Q93K97; -.
DR OMA; TIIALQW; -.
DR PhylomeDB; Q93K97; -.
DR BioCyc; EcoCyc:EG12633-MON; -.
DR BioCyc; MetaCyc:EG12633-MON; -.
DR BRENDA; 3.6.1.13; 2026.
DR EvolutionaryTrace; Q93K97; -.
DR PRO; PR:Q93K97; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0047631; F:ADP-ribose diphosphatase activity; IDA:EcoCyc.
DR GO; GO:0019144; F:ADP-sugar diphosphatase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0016462; F:pyrophosphatase activity; IDA:EcoCyc.
DR GO; GO:0006753; P:nucleoside phosphate metabolic process; IBA:GO_Central.
DR GO; GO:0009408; P:response to heat; IMP:EcoCyc.
DR GO; GO:0019693; P:ribose phosphate metabolic process; IBA:GO_Central.
DR InterPro; IPR004385; NDP_pyrophosphatase.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR TIGRFAMs; TIGR00052; TIGR00052; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Magnesium; Manganese;
KW Metal-binding; Reference proteome.
FT CHAIN 1..209
FT /note="ADP-ribose pyrophosphatase"
FT /id="PRO_0000057042"
FT DOMAIN 55..193
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 97..118
FT /note="Nudix box"
FT ACT_SITE 162
FT /note="Proton acceptor"
FT /evidence="ECO:0000305"
FT BINDING 28..29
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT BINDING 51..52
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT BINDING 56
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT BINDING 79
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT BINDING 96
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 98
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT BINDING 112
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 112
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT BINDING 116
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 116
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT BINDING 133..135
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT BINDING 139
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT BINDING 164
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT CONFLICT 2
FT /note="L -> V (in Ref. 1; CAC44036)"
FT /evidence="ECO:0000305"
FT CONFLICT 6
FT /note="N -> S (in Ref. 1; CAC44036)"
FT /evidence="ECO:0000305"
FT STRAND 8..10
FT /evidence="ECO:0007829|PDB:1G0S"
FT HELIX 13..15
FT /evidence="ECO:0007829|PDB:1G0S"
FT STRAND 16..39
FT /evidence="ECO:0007829|PDB:1G0S"
FT STRAND 49..55
FT /evidence="ECO:0007829|PDB:1G0S"
FT STRAND 59..66
FT /evidence="ECO:0007829|PDB:1G0S"
FT TURN 67..70
FT /evidence="ECO:0007829|PDB:1G0S"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:1G0S"
FT HELIX 80..85
FT /evidence="ECO:0007829|PDB:1G0S"
FT STRAND 89..93
FT /evidence="ECO:0007829|PDB:1G0S"
FT STRAND 95..98
FT /evidence="ECO:0007829|PDB:1G0S"
FT HELIX 105..117
FT /evidence="ECO:0007829|PDB:1G0S"
FT STRAND 124..132
FT /evidence="ECO:0007829|PDB:1G0S"
FT TURN 134..136
FT /evidence="ECO:0007829|PDB:1G0S"
FT STRAND 140..147
FT /evidence="ECO:0007829|PDB:1G0S"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:1G0S"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:1KHZ"
FT TURN 161..165
FT /evidence="ECO:0007829|PDB:1KHZ"
FT STRAND 167..172
FT /evidence="ECO:0007829|PDB:1G0S"
FT HELIX 173..181
FT /evidence="ECO:0007829|PDB:1G0S"
FT HELIX 188..207
FT /evidence="ECO:0007829|PDB:1G0S"
SQ SEQUENCE 209 AA; 23667 MW; 2CF77EA9D63B9615 CRC64;
MLKPDNLPVT FGKNDVEIIA RETLYRGFFS LDLYRFRHRL FNGQMSHEVR REIFERGHAA
VLLPFDPVRD EVVLIEQIRI AAYDTSETPW LLEMVAGMIE EGESVEDVAR REAIEEAGLI
VKRTKPVLSF LASPGGTSER SSIMVGEVDA TTASGIHGLA DENEDIRVHV VSREQAYQWV
EEGKIDNAAS VIALQWLQLH HQALKNEWA
