E4PD_ECOLI
ID E4PD_ECOLI Reviewed; 339 AA.
AC P0A9B6; P11603; Q2M9R5;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=D-erythrose-4-phosphate dehydrogenase;
DE Short=E4PDH;
DE EC=1.2.1.72;
GN Name=epd; Synonyms=gapB; OrderedLocusNames=b2927, JW2894;
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 / CS520;
RX PubMed=2546007; DOI=10.1111/j.1365-2958.1989.tb00221.x;
RA Alefounder P.R., Perham R.N.;
RT "Identification, molecular cloning and sequence analysis of a gene cluster
RT encoding the class II fructose 1,6-bisphosphate aldolase, 3-
RT phosphoglycerate kinase and a putative second glyceraldehyde 3-phosphate
RT dehydrogenase of Escherichia coli.";
RL Mol. Microbiol. 3:723-732(1989).
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 PROTEIN SEQUENCE OF 2-13, CATALYTIC ACTIVITY, SUBUNIT, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12;
RX PubMed=7751290; DOI=10.1128/jb.177.10.2804-2812.1995;
RA Zhao G., Pease A.J., Bharani N., Winkler M.E.;
RT "Biochemical characterization of gapB-encoded erythrose 4-phosphate
RT dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal
RT 5'-phosphate biosynthesis.";
RL J. Bacteriol. 177:2804-2812(1995).
RN [5]
RP GENE TRANSFER DISCUSSION.
RX PubMed=2124629; DOI=10.1007/bf02106053;
RA Doolittle R.F., Feng D.F., Anderson K.L., Alberro M.R.;
RT "A naturally occurring horizontal gene transfer from a eukaryote to a
RT prokaryote.";
RL J. Mol. Evol. 31:383-388(1990).
RN [6]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF CYS-155; HIS-182
RP AND CYS-316, MASS SPECTROMETRY, AND REACTION MECHANISM.
RX PubMed=9182530; DOI=10.1074/jbc.272.24.15106;
RA Boschi-Muller S., Azza S., Pollastro D., Corbier C., Branlant G.;
RT "Comparative enzymatic properties of GapB-encoded erythrose-4-phosphate
RT dehydrogenase of Escherichia coli and phosphorylating glyceraldehyde-3-
RT phosphate dehydrogenase.";
RL J. Biol. Chem. 272:15106-15112(1997).
RN [7]
RP ROLE IN PNP BIOSYNTHESIS.
RX PubMed=9696782; DOI=10.1128/jb.180.16.4294-4299.1998;
RA Yang Y., Zhao G., Man T.-K., Winkler M.E.;
RT "Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in
RT pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12.";
RL J. Bacteriol. 180:4294-4299(1998).
CC -!- FUNCTION: Catalyzes the NAD-dependent conversion of D-erythrose 4-
CC phosphate to 4-phosphoerythronate. {ECO:0000269|PubMed:9182530,
CC ECO:0000269|PubMed:9696782}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-erythrose 4-phosphate + H2O + NAD(+) = 4-phospho-D-
CC erythronate + 2 H(+) + NADH; Xref=Rhea:RHEA:12056, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16897, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:58766; EC=1.2.1.72;
CC Evidence={ECO:0000269|PubMed:7751290};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=74 uM for NAD (at 37 degrees Celsius and pH 8.6)
CC {ECO:0000269|PubMed:7751290, ECO:0000269|PubMed:9182530};
CC KM=510 uM for D-erythrose 4-phosphate (at 25 degrees Celsius and pH
CC 8.9) {ECO:0000269|PubMed:7751290, ECO:0000269|PubMed:9182530};
CC KM=960 uM for D-erythrose 4-phosphate (at 37 degrees Celsius and pH
CC 8.6) {ECO:0000269|PubMed:7751290, ECO:0000269|PubMed:9182530};
CC KM=1100 uM for glyceraldehyde 3-phosphate (at 25 degrees Celsius and
CC pH 8.9) {ECO:0000269|PubMed:7751290, ECO:0000269|PubMed:9182530};
CC Vmax=91.2 umol/min/mg enzyme toward D-erythrose 4-phosphate (at 37
CC degrees Celsius and pH 8.6) {ECO:0000269|PubMed:7751290,
CC ECO:0000269|PubMed:9182530};
CC Vmax=77.2 umol/min/mg enzyme toward NAD (at 37 degrees Celsius and pH
CC 8.6) {ECO:0000269|PubMed:7751290, ECO:0000269|PubMed:9182530};
CC pH dependence:
CC Optimum pH is about 8.6. {ECO:0000269|PubMed:7751290,
CC ECO:0000269|PubMed:9182530};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius at pH 8.6. Relatively
CC thermostable. Activity begins to decrease significantly when E4PDH is
CC incubated at 50 degrees Celsius for 5 min.
CC {ECO:0000269|PubMed:7751290, ECO:0000269|PubMed:9182530};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis;
CC pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 1/5.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:7751290}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- MASS SPECTROMETRY: Mass=37170; Method=Unknown;
CC Evidence={ECO:0000269|PubMed:9182530};
CC -!- SIMILARITY: Belongs to the glyceraldehyde-3-phosphate dehydrogenase
CC family. Epd subfamily. {ECO:0000305}.
CC -!- CAUTION: Was originally (PubMed:2546007 and PubMed:2124629) thought to
CC be a glyceraldehyde 3-phosphate dehydrogenase, but glyceraldehyde 3-
CC phosphate is not an efficient substrate (PubMed:7751290 and
CC PubMed:9182530). {ECO:0000305}.
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DR EMBL; X14436; CAA32603.1; -; Genomic_DNA.
DR EMBL; U28377; AAA69094.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75964.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76991.1; -; Genomic_DNA.
DR PIR; S04732; DEECGB.
DR RefSeq; NP_417402.1; NC_000913.3.
DR RefSeq; WP_000218480.1; NZ_SSZK01000003.1.
DR PDB; 2X5J; X-ray; 2.30 A; O/P/Q/R=1-339.
DR PDB; 2X5K; X-ray; 2.37 A; O/P/Q/R=1-339.
DR PDB; 2XF8; X-ray; 2.95 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P=2-339.
DR PDBsum; 2X5J; -.
DR PDBsum; 2X5K; -.
DR PDBsum; 2XF8; -.
DR AlphaFoldDB; P0A9B6; -.
DR SMR; P0A9B6; -.
DR BioGRID; 4262067; 12.
DR DIP; DIP-9520N; -.
DR IntAct; P0A9B6; 2.
DR STRING; 511145.b2927; -.
DR jPOST; P0A9B6; -.
DR PaxDb; P0A9B6; -.
DR PRIDE; P0A9B6; -.
DR EnsemblBacteria; AAC75964; AAC75964; b2927.
DR EnsemblBacteria; BAE76991; BAE76991; BAE76991.
DR GeneID; 66673196; -.
DR GeneID; 947413; -.
DR KEGG; ecj:JW2894; -.
DR KEGG; eco:b2927; -.
DR PATRIC; fig|1411691.4.peg.3805; -.
DR EchoBASE; EB0363; -.
DR eggNOG; COG0057; Bacteria.
DR HOGENOM; CLU_030140_0_2_6; -.
DR InParanoid; P0A9B6; -.
DR OMA; NAKVLAW; -.
DR PhylomeDB; P0A9B6; -.
DR BioCyc; EcoCyc:ERYTH4PDEHYDROG-MON; -.
DR BioCyc; MetaCyc:ERYTH4PDEHYDROG-MON; -.
DR BRENDA; 1.2.1.72; 2026.
DR SABIO-RK; P0A9B6; -.
DR UniPathway; UPA00244; UER00309.
DR EvolutionaryTrace; P0A9B6; -.
DR PRO; PR:P0A9B6; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0048001; F:erythrose-4-phosphate dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0004365; F:glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity; IDA:EcoCyc.
DR GO; GO:0051287; F:NAD binding; IDA:EcoCyc.
DR GO; GO:0006006; P:glucose metabolic process; IDA:EcoCyc.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IDA:EcoCyc.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IMP:EcoCyc.
DR HAMAP; MF_01640; E4P_dehydrog; 1.
DR InterPro; IPR006422; E4P_DH_bac.
DR InterPro; IPR020831; GlycerAld/Erythrose_P_DH.
DR InterPro; IPR020830; GlycerAld_3-P_DH_AS.
DR InterPro; IPR020829; GlycerAld_3-P_DH_cat.
DR InterPro; IPR020828; GlycerAld_3-P_DH_NAD(P)-bd.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR43148; PTHR43148; 1.
DR Pfam; PF02800; Gp_dh_C; 1.
DR Pfam; PF00044; Gp_dh_N; 1.
DR PIRSF; PIRSF000149; GAP_DH; 1.
DR PRINTS; PR00078; G3PDHDRGNASE.
DR SMART; SM00846; Gp_dh_N; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01532; E4PD_g-proteo; 1.
DR PROSITE; PS00071; GAPDH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; NAD; Oxidoreductase;
KW Pyridoxine biosynthesis; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7751290"
FT CHAIN 2..339
FT /note="D-erythrose-4-phosphate dehydrogenase"
FT /id="PRO_0000145650"
FT ACT_SITE 155
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 12..13
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 81
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 154..156
FT /ligand="substrate"
FT /evidence="ECO:0000255"
FT BINDING 200
FT /ligand="substrate"
FT /evidence="ECO:0000255"
FT BINDING 213..214
FT /ligand="substrate"
FT /evidence="ECO:0000255"
FT BINDING 236
FT /ligand="substrate"
FT /evidence="ECO:0000255"
FT BINDING 318
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT SITE 182
FT /note="Activates thiol group during catalysis"
FT /evidence="ECO:0000250"
FT MUTAGEN 155
FT /note="C->A,G,V: No significant activity."
FT /evidence="ECO:0000269|PubMed:9182530"
FT MUTAGEN 182
FT /note="H->N: 10-fold reduction in activity. Increases
FT affinity for D-erythrose-4-phosphate and reduces affinity
FT for glyceraldehyde 3-phosphate."
FT /evidence="ECO:0000269|PubMed:9182530"
FT MUTAGEN 316
FT /note="C->A,Y: Reduces activity and affinity for D-
FT erythrose-4-phosphate and increases affinity for
FT glyceraldehyde 3-phosphate."
FT /evidence="ECO:0000269|PubMed:9182530"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 12..23
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 26..28
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 30..36
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 41..49
FT /evidence="ECO:0007829|PDB:2X5J"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 73..78
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 88..91
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 94..98
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 100..102
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 106..114
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 118..124
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 130..133
FT /evidence="ECO:0007829|PDB:2X5J"
FT TURN 136..138
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 140..142
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 149..151
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 155..171
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 173..182
FT /evidence="ECO:0007829|PDB:2X5J"
FT TURN 198..201
FT /evidence="ECO:0007829|PDB:2X5J"
FT TURN 204..206
FT /evidence="ECO:0007829|PDB:2XF8"
FT STRAND 209..211
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 215..222
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 229..236
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 243..253
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 257..269
FT /evidence="ECO:0007829|PDB:2X5J"
FT TURN 270..275
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 276..279
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 285..288
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 293..305
FT /evidence="ECO:0007829|PDB:2X5J"
FT TURN 306..308
FT /evidence="ECO:0007829|PDB:2X5J"
FT STRAND 309..316
FT /evidence="ECO:0007829|PDB:2X5J"
FT HELIX 318..334
FT /evidence="ECO:0007829|PDB:2X5J"
SQ SEQUENCE 339 AA; 37299 MW; 4CFC4BD2267EA2A2 CRC64;
MTVRVAINGF GRIGRNVVRA LYESGRRAEI TVVAINELAD AAGMAHLLKY DTSHGRFAWE
VRQERDQLFV GDDAIRVLHE RSLQSLPWRE LGVDVVLDCT GVYGSREHGE AHIAAGAKKV
LFSHPGSNDL DATVVYGVNQ DQLRAEHRIV SNASCTTNCI IPVIKLLDDA YGIESGTVTT
IHSAMHDQQV IDAYHPDLRR TRAASQSIIP VDTKLAAGIT RFFPQFNDRF EAIAVRVPTI
NVTAIDLSVT VKKPVKANEV NLLLQKAAQG AFHGIVDYTE LPLVSVDFNH DPHSAIVDGT
QTRVSGAHLI KTLVWCDNEW GFANRMLDTT LAMATVAFR
