ID NUDE_ECOLI Reviewed; 186 AA.
AC P45799; Q2M762;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 24-JAN-2024, entry version 164.
DE RecName: Full=ADP compounds hydrolase NudE;
DE EC=3.6.1.-;
GN Name=nudE; Synonyms=yrfE; OrderedLocusNames=b3397, JW3360;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
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 [2]
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 [3]
RP CHARACTERIZATION.
RX PubMed=9452430; DOI=10.1074/jbc.273.6.3192;
RA O'Handley S.F., Frick D.N., Dunn C.A., Bessman M.J.;
RT "Orf186 represents a new member of the Nudix hydrolases, active on
RT adenosine(5')triphospho(5')adenosine, ADP-ribose, and NADH.";
RL J. Biol. Chem. 273:3192-3197(1998).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 2-186 IN COMPLEX WITH SUBSTRATE,
RP AND SUBUNIT.
RX PubMed=16021622; DOI=10.1002/prot.20541;
RA Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G.,
RA Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S.,
RA Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D.,
RA Hendle J., Huber A., Hoda K., Kearins P., Kissinger C., Laubert B.,
RA Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M.,
RA Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M.,
RA Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S.,
RA Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J.,
RA Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R.;
RT "Structural analysis of a set of proteins resulting from a bacterial
RT genomics project.";
RL Proteins 60:787-796(2005).
CC -!- FUNCTION: Active on adenosine(5')triphospho(5')adenosine (Ap3A), ADP-
CC ribose, NADH, adenosine(5')diphospho(5')adenosine (Ap2A).
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 -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Mg(2+). Other divalent cations can also be used.;
CC -!- SUBUNIT: Homodimer. {ECO:0000305|PubMed:16021622}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
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DR EMBL; U18997; AAA58194.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76422.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77894.1; -; Genomic_DNA.
DR PIR; H65134; H65134.
DR RefSeq; NP_417856.1; NC_000913.3.
DR RefSeq; WP_000045744.1; NZ_STEB01000004.1.
DR PDB; 1VHG; X-ray; 2.70 A; A/B=2-186.
DR PDB; 1VHZ; X-ray; 2.32 A; A/B=2-186.
DR PDBsum; 1VHG; -.
DR PDBsum; 1VHZ; -.
DR AlphaFoldDB; P45799; -.
DR SMR; P45799; -.
DR BioGRID; 4261276; 223.
DR IntAct; P45799; 1.
DR STRING; 511145.b3397; -.
DR DrugBank; DB02059; Adenosine-5-Diphosphoribose.
DR jPOST; P45799; -.
DR PaxDb; 511145-b3397; -.
DR EnsemblBacteria; AAC76422; AAC76422; b3397.
DR GeneID; 75206335; -.
DR GeneID; 947906; -.
DR KEGG; ecj:JW3360; -.
DR KEGG; eco:b3397; -.
DR PATRIC; fig|1411691.4.peg.3333; -.
DR EchoBASE; EB2762; -.
DR eggNOG; COG0494; Bacteria.
DR HOGENOM; CLU_062658_4_0_6; -.
DR InParanoid; P45799; -.
DR OMA; VRWPLAQ; -.
DR OrthoDB; 9806150at2; -.
DR PhylomeDB; P45799; -.
DR BioCyc; EcoCyc:G7740-MONOMER; -.
DR BioCyc; MetaCyc:G7740-MONOMER; -.
DR EvolutionaryTrace; P45799; -.
DR PRO; PR:P45799; -.
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; IEA:RHEA.
DR GO; GO:0019144; F:ADP-sugar diphosphatase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:EcoCyc.
DR GO; GO:0006753; P:nucleoside phosphate metabolic process; IBA:GO_Central.
DR GO; GO:0019693; P:ribose phosphate metabolic process; IBA:GO_Central.
DR CDD; cd03424; ADPRase_NUDT5; 1.
DR Gene3D; 3.90.79.10; Nucleoside Triphosphate Pyrophosphohydrolase; 1.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR PANTHER; PTHR11839:SF12; ADP COMPOUNDS HYDROLASE NUDE; 1.
DR PANTHER; PTHR11839; UDP/ADP-SUGAR PYROPHOSPHATASE; 1.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; Nudix; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..186
FT /note="ADP compounds hydrolase NudE"
FT /id="PRO_0000056989"
FT DOMAIN 45..172
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 80..101
FT /note="Nudix box"
FT BINDING 40
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16021622"
FT BINDING 95
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 99
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 118
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16021622"
FT STRAND 9..18
FT /evidence="ECO:0007829|PDB:1VHZ"
FT STRAND 23..30
FT /evidence="ECO:0007829|PDB:1VHZ"
FT STRAND 36..42
FT /evidence="ECO:0007829|PDB:1VHZ"
FT STRAND 49..56
FT /evidence="ECO:0007829|PDB:1VHZ"
FT STRAND 59..67
FT /evidence="ECO:0007829|PDB:1VHZ"
FT TURN 68..71
FT /evidence="ECO:0007829|PDB:1VHZ"
FT STRAND 72..76
FT /evidence="ECO:0007829|PDB:1VHZ"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:1VHZ"
FT HELIX 88..100
FT /evidence="ECO:0007829|PDB:1VHZ"
FT STRAND 101..114
FT /evidence="ECO:0007829|PDB:1VHZ"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:1VHZ"
FT STRAND 123..134
FT /evidence="ECO:0007829|PDB:1VHZ"
FT STRAND 147..151
FT /evidence="ECO:0007829|PDB:1VHZ"
FT HELIX 152..160
FT /evidence="ECO:0007829|PDB:1VHZ"
FT TURN 162..164
FT /evidence="ECO:0007829|PDB:1VHZ"
FT HELIX 167..182
FT /evidence="ECO:0007829|PDB:1VHZ"
SQ SEQUENCE 186 AA; 21153 MW; D959AD8ECF73FCC4 CRC64;
MSKSLQKPTI LNVETVARSR LFTVESVDLE FSNGVRRVYE RMRPTNREAV MIVPIVDDHL
ILIREYAVGT ESYELGFSKG LIDPGESVYE AANRELKEEV GFGANDLTFL KKLSMAPSYF
SSKMNIVVAQ DLYPESLEGD EPEPLPQVRW PLAHMMDLLE DPDFNEARNV SALFLVREWL
KGQGRV
//
