NUDB_ECOLI
ID NUDB_ECOLI Reviewed; 150 AA.
AC P0AFC0; P24236;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Dihydroneopterin triphosphate diphosphatase;
DE EC=3.6.1.67 {ECO:0000269|PubMed:8798731};
DE AltName: Full=Dihydroneopterin triphosphate pyrophosphatase;
DE AltName: Full=dATP pyrophosphohydrolase;
GN Name=nudB; Synonyms=ntpA; OrderedLocusNames=b1865, JW1854;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1657895; DOI=10.1128/jb.173.23.7711-7715.1991;
RA Sharples G.J., Lloyd R.G.;
RT "Resolution of Holliday junctions in Escherichia coli: identification of
RT the ruvC gene product as a 19-kilodalton protein.";
RL J. Bacteriol. 173:7711-7715(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1885548; DOI=10.1128/jb.173.18.5747-5753.1991;
RA Takahagi M., Iwasaki H., Nakata A., Shinagawa H.;
RT "Molecular analysis of the Escherichia coli ruvC gene, which encodes a
RT Holliday junction-specific endonuclease.";
RL J. Bacteriol. 173:5747-5753(1991).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA Horiuchi T.;
RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 40.1-50.0 min region on the linkage map.";
RL DNA Res. 3:379-392(1996).
RN [4]
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 [5]
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 [6]
RP CHARACTERIZATION.
RX PubMed=8163538; DOI=10.1016/s0021-9258(17)32721-7;
RA Bullions L.C., Mejean V., Claverys J.-P., Bessman M.J.;
RT "Purification of the MutX protein of Streptococcus pneumoniae, a homologue
RT of Escherichia coli MutT. Identification of a novel catalytic domain for
RT nucleoside triphosphate pyrophosphohydrolase activity.";
RL J. Biol. Chem. 269:12339-12344(1994).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND COFACTOR.
RX PubMed=8798731; DOI=10.1074/jbc.271.40.24649;
RA O'Handley S.F., Frick D.N., Bullions L.C., Mildvan A.S., Bessman M.J.;
RT "Escherichia coli orf17 codes for a nucleoside triphosphate
RT pyrophosphohydrolase member of the MutT family of proteins. Cloning,
RT purification, and characterization of the enzyme.";
RL J. Biol. Chem. 271:24649-24654(1996).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH PYROPHOSPHATE AND
RP SAMARIUM IONS, FUNCTION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=17698004; DOI=10.1016/j.str.2007.06.018;
RA Gabelli S.B., Bianchet M.A., Xu W., Dunn C.A., Niu Z.-D., Amzel L.M.,
RA Bessman M.J.;
RT "Structure and function of the E. coli dihydroneopterin triphosphate
RT pyrophosphatase: a Nudix enzyme involved in folate biosynthesis.";
RL Structure 15:1014-1022(2007).
CC -!- FUNCTION: Catalyzes the hydrolysis of dihydroneopterin triphosphate to
CC dihydroneopterin monophosphate and pyrophosphate. Required for
CC efficient folate biosynthesis. Can also hydrolyze nucleoside
CC triphosphates with a preference for dATP. {ECO:0000269|PubMed:17698004,
CC ECO:0000269|PubMed:8798731}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=7,8-dihydroneopterin 3'-triphosphate + H2O = 7,8-
CC dihydroneopterin 3'-phosphate + diphosphate + H(+);
CC Xref=Rhea:RHEA:25302, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:58462, ChEBI:CHEBI:58762; EC=3.6.1.67;
CC Evidence={ECO:0000269|PubMed:8798731};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:8798731};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:8798731};
CC -!- ACTIVITY REGULATION: Subject to product inhibition by pyrophosphate.
CC {ECO:0000269|PubMed:8798731}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.27 mM for dihydroneopterin triphosphate
CC {ECO:0000269|PubMed:17698004, ECO:0000269|PubMed:8798731};
CC KM=0.79 mM for dATP {ECO:0000269|PubMed:17698004,
CC ECO:0000269|PubMed:8798731};
CC pH dependence:
CC Optimum pH is 8.5-9. {ECO:0000269|PubMed:17698004,
CC ECO:0000269|PubMed:8798731};
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
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DR EMBL; X59551; CAA42124.1; -; Genomic_DNA.
DR EMBL; D10165; BAA01029.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74935.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15676.1; -; Genomic_DNA.
DR PIR; B38113; B38113.
DR RefSeq; NP_416379.1; NC_000913.3.
DR RefSeq; WP_001300367.1; NZ_SSZK01000001.1.
DR PDB; 2O1C; X-ray; 1.80 A; A/B/C/D=1-150.
DR PDB; 2O5W; X-ray; 2.60 A; A/B/C/D=1-150.
DR PDBsum; 2O1C; -.
DR PDBsum; 2O5W; -.
DR AlphaFoldDB; P0AFC0; -.
DR SMR; P0AFC0; -.
DR BioGRID; 4260348; 315.
DR DIP; DIP-10372N; -.
DR IntAct; P0AFC0; 7.
DR STRING; 511145.b1865; -.
DR PaxDb; P0AFC0; -.
DR PRIDE; P0AFC0; -.
DR EnsemblBacteria; AAC74935; AAC74935; b1865.
DR EnsemblBacteria; BAA15676; BAA15676; BAA15676.
DR GeneID; 58389836; -.
DR GeneID; 946383; -.
DR KEGG; ecj:JW1854; -.
DR KEGG; eco:b1865; -.
DR PATRIC; fig|511145.12.peg.1944; -.
DR EchoBASE; EB1128; -.
DR eggNOG; COG0494; Bacteria.
DR HOGENOM; CLU_128620_0_0_6; -.
DR InParanoid; P0AFC0; -.
DR OMA; NTEHVFG; -.
DR PhylomeDB; P0AFC0; -.
DR BioCyc; EcoCyc:H2NEOPTERINP3PYROPHOSPHOHYDRO-MON; -.
DR BioCyc; MetaCyc:H2NEOPTERINP3PYROPHOSPHOHYDRO-MON; -.
DR BRENDA; 3.6.1.67; 2026.
DR EvolutionaryTrace; P0AFC0; -.
DR PRO; PR:P0AFC0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008828; F:dATP pyrophosphohydrolase activity; IDA:EcoCyc.
DR GO; GO:0019177; F:dihydroneopterin triphosphate pyrophosphohydrolase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IDA:EcoCyc.
DR GO; GO:0046656; P:folic acid biosynthetic process; IMP:EcoCyc.
DR GO; GO:0046654; P:tetrahydrofolate biosynthetic process; IMP:EcoCyc.
DR InterPro; IPR003564; DHNTPase.
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 PRINTS; PR01404; NPPPHYDRLASE.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Folate biosynthesis; Hydrolase; Magnesium; Metal-binding;
KW Reference proteome.
FT CHAIN 1..150
FT /note="Dihydroneopterin triphosphate diphosphatase"
FT /id="PRO_0000056952"
FT DOMAIN 5..146
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 41..62
FT /note="Nudix box"
FT BINDING 7
FT /ligand="substrate"
FT BINDING 29
FT /ligand="substrate"
FT BINDING 40
FT /ligand="substrate"
FT BINDING 56
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 60
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 81..84
FT /ligand="substrate"
FT /evidence="ECO:0000255"
FT BINDING 117
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 135
FT /ligand="substrate"
FT /evidence="ECO:0000255"
FT STRAND 9..18
FT /evidence="ECO:0007829|PDB:2O1C"
FT TURN 19..21
FT /evidence="ECO:0007829|PDB:2O1C"
FT STRAND 23..28
FT /evidence="ECO:0007829|PDB:2O1C"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:2O1C"
FT STRAND 36..42
FT /evidence="ECO:0007829|PDB:2O1C"
FT HELIX 49..61
FT /evidence="ECO:0007829|PDB:2O1C"
FT HELIX 65..68
FT /evidence="ECO:0007829|PDB:2O1C"
FT STRAND 72..82
FT /evidence="ECO:0007829|PDB:2O1C"
FT HELIX 85..90
FT /evidence="ECO:0007829|PDB:2O1C"
FT STRAND 97..109
FT /evidence="ECO:0007829|PDB:2O1C"
FT STRAND 116..119
FT /evidence="ECO:0007829|PDB:2O1C"
FT STRAND 121..125
FT /evidence="ECO:0007829|PDB:2O1C"
FT HELIX 126..132
FT /evidence="ECO:0007829|PDB:2O1C"
FT HELIX 136..145
FT /evidence="ECO:0007829|PDB:2O1C"
SQ SEQUENCE 150 AA; 17306 MW; B4F05FA056F3BA07 CRC64;
MKDKVYKRPV SILVVIYAQD TKRVLMLQRR DDPDFWQSVT GSVEEGETAP QAAMREVKEE
VTIDVVAEQL TLIDCQRTVE FEIFSHLRHR YAPGVTRNTE SWFCLALPHE RQIVFTEHLA
YKWLDAPAAA ALTKSWSNRQ AIEQFVINAA
