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Protein

D-erythrose-4-phosphate dehydrogenase

Gene

epd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the NAD-dependent conversion of D-erythrose 4-phosphate to 4-phosphoerythronate.2 Publications

Catalytic activityi

D-erythrose 4-phosphate + NAD+ + H2O = 4-phosphoerythronate + NADH.1 Publication

Kineticsi

  1. KM=74 µM for NAD (at 37 degrees Celsius and pH 8.6)2 Publications
  2. KM=510 µM for D-erythrose 4-phosphate (at 25 degrees Celsius and pH 8.9)2 Publications
  3. KM=960 µM for D-erythrose 4-phosphate (at 37 degrees Celsius and pH 8.6)2 Publications
  4. KM=1100 µM for glyceraldehyde 3-phosphate (at 25 degrees Celsius and pH 8.9)2 Publications
  1. Vmax=91.2 µmol/min/mg enzyme toward D-erythrose 4-phosphate (at 37 degrees Celsius and pH 8.6)2 Publications
  2. Vmax=77.2 µmol/min/mg enzyme toward NAD (at 37 degrees Celsius and pH 8.6)2 Publications

pH dependencei

Optimum pH is about 8.6.2 Publications

Temperature dependencei

Optimum temperature is 50 degrees Celsius at pH 8.6. Relatively thermostable. Activity begins to decrease significantly when E4PDH is incubated at 50 degrees Celsius for 5 min.2 Publications

Pathwayi: pyridoxine 5'-phosphate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. D-erythrose-4-phosphate dehydrogenase (epd)
  2. Erythronate-4-phosphate dehydrogenase (pdxB)
  3. Phosphoserine aminotransferase (serC)
  4. 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA)
  5. Pyridoxine 5'-phosphate synthase (pdxJ)
This subpathway is part of the pathway pyridoxine 5'-phosphate biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate, the pathway pyridoxine 5'-phosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei81 – 811NAD; via carbonyl oxygenBy similarity
Active sitei155 – 1551NucleophileBy similarity
Sitei182 – 1821Activates thiol group during catalysisBy similarity
Binding sitei200 – 2001SubstrateSequence analysis
Binding sitei236 – 2361SubstrateSequence analysis
Binding sitei318 – 3181NADBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi12 – 132NADBy similarity

GO - Molecular functioni

  • erythrose-4-phosphate dehydrogenase activity Source: EcoCyc
  • glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity Source: EcoCyc
  • NAD binding Source: EcoCyc

GO - Biological processi

  • glucose metabolic process Source: EcoCyc
  • pyridoxal phosphate biosynthetic process Source: EcoCyc
  • pyridoxine biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciEcoCyc:ERYTH4PDEHYDROG-MONOMER.
ECOL316407:JW2894-MONOMER.
MetaCyc:ERYTH4PDEHYDROG-MONOMER.
BRENDAi1.2.1.72. 2026.
SABIO-RKP0A9B6.
UniPathwayiUPA00244; UER00309.

Names & Taxonomyi

Protein namesi
Recommended name:
D-erythrose-4-phosphate dehydrogenase (EC:1.2.1.72)
Short name:
E4PDH
Gene namesi
Name:epd
Synonyms:gapB
Ordered Locus Names:b2927, JW2894
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10368. epd.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi155 – 1551C → A, G or V: No significant activity. 1 Publication
Mutagenesisi182 – 1821H → N: 10-fold reduction in activity. Increases affinity for D-erythrose-4-phosphate and reduces affinity for glyceraldehyde 3-phosphate. 1 Publication
Mutagenesisi316 – 3161C → A or Y: Reduces activity and affinity for D-erythrose-4-phosphate and increases affinity for glyceraldehyde 3-phosphate. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 339338D-erythrose-4-phosphate dehydrogenasePRO_0000145650Add
BLAST

Proteomic databases

PaxDbiP0A9B6.
PRIDEiP0A9B6.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

BioGridi4262067. 5 interactions.
DIPiDIP-9520N.
IntActiP0A9B6. 2 interactions.
STRINGi511145.b2927.

Structurei

Secondary structure

1
339
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi12 – 2312Combined sources
Helixi26 – 283Combined sources
Beta strandi30 – 367Combined sources
Helixi41 – 499Combined sources
Turni52 – 543Combined sources
Beta strandi61 – 644Combined sources
Beta strandi67 – 704Combined sources
Beta strandi73 – 786Combined sources
Helixi83 – 853Combined sources
Helixi88 – 914Combined sources
Beta strandi94 – 985Combined sources
Beta strandi100 – 1023Combined sources
Helixi106 – 1149Combined sources
Beta strandi118 – 1247Combined sources
Beta strandi130 – 1334Combined sources
Turni136 – 1383Combined sources
Helixi140 – 1423Combined sources
Beta strandi149 – 1513Combined sources
Helixi155 – 17117Combined sources
Beta strandi173 – 18210Combined sources
Turni198 – 2014Combined sources
Turni204 – 2063Combined sources
Beta strandi209 – 2113Combined sources
Helixi215 – 2228Combined sources
Helixi224 – 2263Combined sources
Beta strandi229 – 2368Combined sources
Beta strandi243 – 25311Combined sources
Helixi257 – 26913Combined sources
Turni270 – 2756Combined sources
Beta strandi276 – 2794Combined sources
Helixi285 – 2884Combined sources
Beta strandi293 – 30513Combined sources
Turni306 – 3083Combined sources
Beta strandi309 – 3168Combined sources
Helixi318 – 33417Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2X5JX-ray2.30O/P/Q/R1-339[»]
2X5KX-ray2.37O/P/Q/R1-339[»]
2XF8X-ray2.95A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P2-339[»]
ProteinModelPortaliP0A9B6.
SMRiP0A9B6. Positions 2-339.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A9B6.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni154 – 1563Substrate bindingSequence analysis
Regioni213 – 2142Substrate bindingSequence analysis

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C17. Bacteria.
COG0057. LUCA.
HOGENOMiHOG000071679.
InParanoidiP0A9B6.
KOiK03472.
OMAiYLEYTEL.
PhylomeDBiP0A9B6.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_01640. E4P_dehydrog. 1 hit.
InterProiIPR006422. E4P_DH_bac.
IPR020831. GlycerAld/Erythrose_P_DH.
IPR020830. GlycerAld_3-P_DH_AS.
IPR020829. GlycerAld_3-P_DH_cat.
IPR020828. GlycerAld_3-P_DH_NAD(P)-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR10836. PTHR10836. 1 hit.
PfamiPF02800. Gp_dh_C. 1 hit.
PF00044. Gp_dh_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000149. GAP_DH. 1 hit.
PRINTSiPR00078. G3PDHDRGNASE.
SMARTiSM00846. Gp_dh_N. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01532. E4PD_g-proteo. 1 hit.
PROSITEiPS00071. GAPDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A9B6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTVRVAINGF GRIGRNVVRA LYESGRRAEI TVVAINELAD AAGMAHLLKY
60 70 80 90 100
DTSHGRFAWE VRQERDQLFV GDDAIRVLHE RSLQSLPWRE LGVDVVLDCT
110 120 130 140 150
GVYGSREHGE AHIAAGAKKV LFSHPGSNDL DATVVYGVNQ DQLRAEHRIV
160 170 180 190 200
SNASCTTNCI IPVIKLLDDA YGIESGTVTT IHSAMHDQQV IDAYHPDLRR
210 220 230 240 250
TRAASQSIIP VDTKLAAGIT RFFPQFNDRF EAIAVRVPTI NVTAIDLSVT
260 270 280 290 300
VKKPVKANEV NLLLQKAAQG AFHGIVDYTE LPLVSVDFNH DPHSAIVDGT
310 320 330
QTRVSGAHLI KTLVWCDNEW GFANRMLDTT LAMATVAFR
Length:339
Mass (Da):37,299
Last modified:January 23, 2007 - v2
Checksum:i4CFC4BD2267EA2A2
GO

Mass spectrometryi

Molecular mass is 37170 Da from positions 2 - 339. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X14436 Genomic DNA. Translation: CAA32603.1.
U28377 Genomic DNA. Translation: AAA69094.1.
U00096 Genomic DNA. Translation: AAC75964.1.
AP009048 Genomic DNA. Translation: BAE76991.1.
PIRiS04732. DEECGB.
RefSeqiNP_417402.1. NC_000913.3.
WP_000218480.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75964; AAC75964; b2927.
BAE76991; BAE76991; BAE76991.
GeneIDi947413.
KEGGiecj:JW2894.
eco:b2927.
PATRICi32121268. VBIEscCol129921_3022.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X14436 Genomic DNA. Translation: CAA32603.1.
U28377 Genomic DNA. Translation: AAA69094.1.
U00096 Genomic DNA. Translation: AAC75964.1.
AP009048 Genomic DNA. Translation: BAE76991.1.
PIRiS04732. DEECGB.
RefSeqiNP_417402.1. NC_000913.3.
WP_000218480.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2X5JX-ray2.30O/P/Q/R1-339[»]
2X5KX-ray2.37O/P/Q/R1-339[»]
2XF8X-ray2.95A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P2-339[»]
ProteinModelPortaliP0A9B6.
SMRiP0A9B6. Positions 2-339.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262067. 5 interactions.
DIPiDIP-9520N.
IntActiP0A9B6. 2 interactions.
STRINGi511145.b2927.

Proteomic databases

PaxDbiP0A9B6.
PRIDEiP0A9B6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75964; AAC75964; b2927.
BAE76991; BAE76991; BAE76991.
GeneIDi947413.
KEGGiecj:JW2894.
eco:b2927.
PATRICi32121268. VBIEscCol129921_3022.

Organism-specific databases

EchoBASEiEB0363.
EcoGeneiEG10368. epd.

Phylogenomic databases

eggNOGiENOG4105C17. Bacteria.
COG0057. LUCA.
HOGENOMiHOG000071679.
InParanoidiP0A9B6.
KOiK03472.
OMAiYLEYTEL.
PhylomeDBiP0A9B6.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00309.
BioCyciEcoCyc:ERYTH4PDEHYDROG-MONOMER.
ECOL316407:JW2894-MONOMER.
MetaCyc:ERYTH4PDEHYDROG-MONOMER.
BRENDAi1.2.1.72. 2026.
SABIO-RKP0A9B6.

Miscellaneous databases

EvolutionaryTraceiP0A9B6.
PROiP0A9B6.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_01640. E4P_dehydrog. 1 hit.
InterProiIPR006422. E4P_DH_bac.
IPR020831. GlycerAld/Erythrose_P_DH.
IPR020830. GlycerAld_3-P_DH_AS.
IPR020829. GlycerAld_3-P_DH_cat.
IPR020828. GlycerAld_3-P_DH_NAD(P)-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR10836. PTHR10836. 1 hit.
PfamiPF02800. Gp_dh_C. 1 hit.
PF00044. Gp_dh_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000149. GAP_DH. 1 hit.
PRINTSiPR00078. G3PDHDRGNASE.
SMARTiSM00846. Gp_dh_N. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01532. E4PD_g-proteo. 1 hit.
PROSITEiPS00071. GAPDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiE4PD_ECOLI
AccessioniPrimary (citable) accession number: P0A9B6
Secondary accession number(s): P11603, Q2M9R5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 97 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally (PubMed:2546007 and PubMed:2124629) thought to be a glyceraldehyde 3-phosphate dehydrogenase, but glyceraldehyde 3-phosphate is not an efficient substrate (PubMed:7751290 and PubMed:9182530).Curated

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.