NAGD_ECOLI
ID NAGD_ECOLI Reviewed; 250 AA.
AC P0AF24; P15302;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Ribonucleotide monophosphatase NagD;
DE EC=3.1.3.5 {ECO:0000269|PubMed:16430214};
GN Name=nagD; OrderedLocusNames=b0675, JW0661;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2668691; DOI=10.1111/j.1365-2958.1989.tb00197.x;
RA Plumbridge J.;
RT "Sequence of the nagBACD operon in Escherichia coli K12 and pattern of
RT transcription within the nag regulon.";
RL Mol. Microbiol. 3:505-515(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2190615; DOI=10.1139/o90-017;
RA Peri K.G., Goldie H., Waygood E.B.;
RT "Cloning and characterization of the N-acetylglucosamine operon of
RT Escherichia coli.";
RL Biochem. Cell Biol. 68:123-137(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(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 FUNCTION AS A PHOSPHATASE, SUBSTRATE SPECIFICITY, AND COFACTOR.
RX PubMed=16990279; DOI=10.1074/jbc.m605449200;
RA Kuznetsova E., Proudfoot M., Gonzalez C.F., Brown G., Omelchenko M.V.,
RA Borozan I., Carmel L., Wolf Y.I., Mori H., Savchenko A.V., Arrowsmith C.H.,
RA Koonin E.V., Edwards A.M., Yakunin A.F.;
RT "Genome-wide analysis of substrate specificities of the Escherichia coli
RT haloacid dehalogenase-like phosphatase family.";
RL J. Biol. Chem. 281:36149-36161(2006).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH MAGNESIUM IONS,
RP FUNCTION AS A RIBONUCLEOTIDE MONOPHOSPHATASE, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND SUBUNIT.
RX PubMed=16430214; DOI=10.1021/bi051842j;
RA Tremblay L.W., Dunaway-Mariano D., Allen K.N.;
RT "Structure and activity analyses of Escherichia coli K-12 NagD provide
RT insight into the evolution of biochemical function in the haloalkanoic acid
RT dehalogenase superfamily.";
RL Biochemistry 45:1183-1193(2006).
CC -!- FUNCTION: Catalyzes the dephosphorylation of an unusually broad range
CC of substrate including deoxyribo- and ribonucleoside tri-, di-, and
CC monophosphates, as well as polyphosphate and glucose-1-P (Glu1P).
CC {ECO:0000269|PubMed:16430214, ECO:0000269|PubMed:16990279}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-phosphate + H2O = a ribonucleoside +
CC phosphate; Xref=Rhea:RHEA:12484, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:18254, ChEBI:CHEBI:43474, ChEBI:CHEBI:58043; EC=3.1.3.5;
CC Evidence={ECO:0000269|PubMed:16430214};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:16430214, ECO:0000269|PubMed:16990279};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:16430214, ECO:0000269|PubMed:16990279};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:16430214, ECO:0000269|PubMed:16990279};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:16430214, ECO:0000269|PubMed:16990279};
CC Note=Magnesium. Can also use other divalent metal cations as manganese,
CC cobalt or zinc. {ECO:0000269|PubMed:16430214,
CC ECO:0000269|PubMed:16990279};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=160 uM for UMP (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC KM=400 uM for GMP (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC KM=840 uM for AMP (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC KM=840 uM for ribose-5-phosphate (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC KM=1470 uM for CMP (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC KM=1500 uM for dTMP (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC KM=1500 uM for pyridoxal 5-phosphate (at pH 7 and at 25 degrees
CC Celsius) {ECO:0000269|PubMed:16430214};
CC KM=1700 uM for glycerol 3-phosphate (at pH 7 and at 25 degrees
CC Celsius) {ECO:0000269|PubMed:16430214};
CC KM=5900 uM for glucose 6-phosphate (at pH 7 and at 25 degrees
CC Celsius) {ECO:0000269|PubMed:16430214};
CC KM=6000 uM for glucosamine 6-phosphate (at pH 7 and at 25 degrees
CC Celsius) {ECO:0000269|PubMed:16430214};
CC KM=6000 uM for dCMP (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC KM=6500 uM for dAMP (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC KM=7600 uM for dGMP (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC KM=7700 uM for dGMP (at pH 7 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:16430214};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:16430214}.
CC -!- INDUCTION: By N-acetylglucosamine. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. NagD family.
CC {ECO:0000305}.
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DR EMBL; X14135; CAA32355.1; -; Genomic_DNA.
DR EMBL; AF052007; AAC09327.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73769.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35318.1; -; Genomic_DNA.
DR PIR; B64802; B64802.
DR RefSeq; NP_415201.1; NC_000913.3.
DR RefSeq; WP_000153129.1; NZ_STEB01000044.1.
DR RefSeq; WP_000153136.1; NZ_CP014272.1.
DR PDB; 2C4N; X-ray; 1.80 A; A=1-250.
DR PDBsum; 2C4N; -.
DR AlphaFoldDB; P0AF24; -.
DR SMR; P0AF24; -.
DR BioGRID; 4259613; 11.
DR DIP; DIP-6861N; -.
DR IntAct; P0AF24; 4.
DR STRING; 511145.b0675; -.
DR jPOST; P0AF24; -.
DR PaxDb; P0AF24; -.
DR PRIDE; P0AF24; -.
DR EnsemblBacteria; AAC73769; AAC73769; b0675.
DR EnsemblBacteria; BAA35318; BAA35318; BAA35318.
DR GeneID; 67416288; -.
DR GeneID; 945283; -.
DR KEGG; ecj:JW0661; -.
DR KEGG; eco:b0675; -.
DR PATRIC; fig|511145.12.peg.700; -.
DR EchoBASE; EB0628; -.
DR eggNOG; COG0647; Bacteria.
DR HOGENOM; CLU_043473_1_1_6; -.
DR InParanoid; P0AF24; -.
DR OMA; PPMHRET; -.
DR PhylomeDB; P0AF24; -.
DR BioCyc; EcoCyc:EG10634-MON; -.
DR BioCyc; MetaCyc:EG10634-MON; -.
DR EvolutionaryTrace; P0AF24; -.
DR PRO; PR:P0AF24; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0008253; F:5'-nucleotidase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0016791; F:phosphatase activity; IBA:GO_Central.
DR GO; GO:0106411; F:XMP 5'-nucleosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0046050; P:UMP catabolic process; IMP:EcoCyc.
DR Gene3D; 3.40.50.1000; -; 2.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006357; HAD-SF_hydro_IIA.
DR InterPro; IPR023214; HAD_sf.
DR Pfam; PF13344; Hydrolase_6; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01460; HAD-SF-IIA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Hydrolase; Magnesium; Metal-binding;
KW Reference proteome.
FT CHAIN 1..250
FT /note="Ribonucleotide monophosphatase NagD"
FT /id="PRO_0000096694"
FT ACT_SITE 9
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:16430214"
FT ACT_SITE 11
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:16430214"
FT BINDING 9
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16430214,
FT ECO:0007744|PDB:2C4N"
FT BINDING 11
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16430214,
FT ECO:0007744|PDB:2C4N"
FT BINDING 11
FT /ligand="substrate"
FT BINDING 42..43
FT /ligand="substrate"
FT BINDING 176
FT /ligand="substrate"
FT BINDING 201
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16430214,
FT ECO:0007744|PDB:2C4N"
FT BINDING 202..205
FT /ligand="substrate"
FT SITE 55
FT /note="Orients D-11 for proton transfer during catalytic
FT turnover"
FT /evidence="ECO:0000305|PubMed:16430214"
FT SITE 146
FT /note="Confers substrate specificity"
FT CONFLICT 97
FT /note="H -> Y (in Ref. 2; AAC09327)"
FT /evidence="ECO:0000305"
FT STRAND 5..9
FT /evidence="ECO:0007829|PDB:2C4N"
FT TURN 12..14
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 24..33
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 38..43
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 49..58
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 65..67
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 68..70
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 71..80
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 86..90
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 94..101
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 108..110
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 112..116
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 124..135
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 139..143
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 147..150
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 156..167
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 180..189
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 193..195
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 196..201
FT /evidence="ECO:0007829|PDB:2C4N"
FT TURN 203..205
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 206..212
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 216..224
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 227..230
FT /evidence="ECO:0007829|PDB:2C4N"
FT STRAND 238..243
FT /evidence="ECO:0007829|PDB:2C4N"
FT HELIX 244..246
FT /evidence="ECO:0007829|PDB:2C4N"
SQ SEQUENCE 250 AA; 27163 MW; CC256AE6FF58DEBA CRC64;
MTIKNVICDI DGVLMHDNVA VPGAAEFLHG IMDKGLPLVL LTNYPSQTGQ DLANRFATAG
VDVPDSVFYT SAMATADFLR RQEGKKAYVV GEGALIHELY KAGFTITDVN PDFVIVGETR
SYNWDMMHKA AYFVANGARF IATNPDTHGR GFYPACGALC AGIEKISGRK PFYVGKPSPW
IIRAALNKMQ AHSEETVIVG DNLRTDILAG FQAGLETILV LSGVSSLDDI DSMPFRPSWI
YPSVAEIDVI
