D-erythrose-4-phosphate dehydrogenase - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P0A9B6 (E4PD_ECOLI)

Last modified February 9, 2010. Version 47. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    D-erythrose-4-phosphate dehydrogenase
      Short name=E4PDH
    EC=1.2.1.72

Gene names

Name:	epd
Synonyms:	gapB
Ordered Locus Names:	b2927, JW2894

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	339 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Catalyzes the NAD-dependent conversion of D-erythrose 4-phosphate to 4-phosphoerythronate. Ref.6 Ref.7
Catalytic activity	D-erythrose 4-phosphate + NAD⁺ + H₂O = 4-phosphoerythronate + NADH. Ref.4
Pathway	Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 1/5. HAMAP MF_01640
Subunit structure	Homotetramer. Ref.4
Subcellular location	Cytoplasm HAMAP MF_01640.
Sequence similarities	Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. Epd subfamily.
Caution	Was originally (Ref.1 and Ref.5) thought to be a glyceraldehyde 3-phosphate dehydrogenase, but glyceraldehyde 3-phosphate is not an efficient substrate (Ref.4 and Ref.6).
Biophysicochemical properties	Kinetic parameters: K_M=74 µM for NAD (at 37 degrees Celsius and pH 8.6) HAMAP MF_01640 K_M=510 µM for D-erythrose 4-phosphate (at 25 degrees Celsius and pH 8.9) K_M=960 µM for D-erythrose 4-phosphate (at 37 degrees Celsius and pH 8.6) K_M=1100 µM for glyceraldehyde 3-phosphate (at 25 degrees Celsius and pH 8.9) V_max=91.2 µmol/min/mg enzyme toward D-erythrose 4-phosphate (at 37 degrees Celsius and pH 8.6) V_max=77.2 µmol/min/mg enzyme toward NAD (at 37 degrees Celsius and pH 8.6) pH dependence: Optimum pH is about 8.6. Temperature dependence: 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.
Mass spectrometry	Molecular mass is 37170 Da from positions 2 - 339. Ref.6

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Ontologies

Keywords
Biological process	Pyridoxine biosynthesis
Cellular component	Cytoplasm
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	glucose metabolic process Inferred from electronic annotation. Source: InterPro oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW pyridoxal phosphate biosynthetic process Inferred from electronic annotation. Source: HAMAP pyridoxine biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	NAD or NADH binding Inferred from electronic annotation. Source: InterPro erythrose-4-phosphate dehydrogenase activity Inferred from electronic annotation. Source: HAMAP glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity Inferred from electronic annotation. Source: InterPro protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
groL	P0A6F5	1	EBI-1130931,EBI-543750

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.4

Chain

2 – 339

338

D-erythrose-4-phosphate dehydrogenase HAMAP MF_01640

PRO_0000145650

Regions

Nucleotide binding

12 – 13

NAD By similarity

Region

154 – 156

Substrate binding Potential

Region

213 – 214

Substrate binding Potential

Sites

Active site

155

Nucleophile By similarity

Binding site

NAD; via carbonyl oxygen By similarity

Binding site

200

Substrate Potential

Binding site

236

Substrate Potential

Binding site

318

NAD By similarity

Site

182

Activates thiol group during catalysis By similarity

Experimental info

Mutagenesis

155

C → A, G or V: No significant activity. Ref.6

Mutagenesis

182

H → N: 10-fold reduction in activity. Increases affinity for D-erythrose-4-phosphate and reduces affinity for glyceraldehyde 3-phosphate. Ref.6

Mutagenesis

316

C → A or Y: Reduces activity and affinity for D-erythrose-4-phosphate and increases affinity for glyceraldehyde 3-phosphate. Ref.6

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Sequences

Sequence

Length

Mass (Da)

Tools

P0A9B6-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 4CFC4BD2267EA2A2
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FASTA

339

37,299

        10         20         30         40         50         60 
MTVRVAINGF GRIGRNVVRA LYESGRRAEI TVVAINELAD AAGMAHLLKY DTSHGRFAWE 

        70         80         90        100        110        120 
VRQERDQLFV GDDAIRVLHE RSLQSLPWRE LGVDVVLDCT GVYGSREHGE AHIAAGAKKV 

       130        140        150        160        170        180 
LFSHPGSNDL DATVVYGVNQ DQLRAEHRIV SNASCTTNCI IPVIKLLDDA YGIESGTVTT 

       190        200        210        220        230        240 
IHSAMHDQQV IDAYHPDLRR TRAASQSIIP VDTKLAAGIT RFFPQFNDRF EAIAVRVPTI 

       250        260        270        280        290        300 
NVTAIDLSVT VKKPVKANEV NLLLQKAAQG AFHGIVDYTE LPLVSVDFNH DPHSAIVDGT 

       310        320        330 
QTRVSGAHLI KTLVWCDNEW GFANRMLDTT LAMATVAFR

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification, molecular cloning and sequence analysis of a gene cluster encoding the class II fructose 1,6-bisphosphate aldolase, 3-phosphoglycerate kinase and a putative second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli." Alefounder P.R., Perham R.N. Mol. Microbiol. 3:723-732(1989) [PubMed: 2546007] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / CS520.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis." Zhao G., Pease A.J., Bharani N., Winkler M.E. J. Bacteriol. 177:2804-2812(1995) [PubMed: 7751290] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13, CATALYTIC ACTIVITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES. Strain: K12.
[5]	"A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote." Doolittle R.F., Feng D.F., Anderson K.L., Alberro M.R. J. Mol. Evol. 31:383-388(1990) [PubMed: 2124629] [Abstract] Cited for: GENE TRANSFER DISCUSSION.
[6]	"Comparative enzymatic properties of GapB-encoded erythrose-4-phosphate dehydrogenase of Escherichia coli and phosphorylating glyceraldehyde-3-phosphate dehydrogenase." Boschi-Muller S., Azza S., Pollastro D., Corbier C., Branlant G. J. Biol. Chem. 272:15106-15112(1997) [PubMed: 9182530] [Abstract] Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF CYS-155; HIS-182 AND CYS-316, MASS SPECTROMETRY, REACTION MECHANISM.
[7]	"Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12." Yang Y., Zhao G., Man T.-K., Winkler M.E. J. Bacteriol. 180:4294-4299(1998) [PubMed: 9696782] [Abstract] Cited for: ROLE IN PNP BIOSYNTHESIS.

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Cross-references

Sequence databases
EMBL GenBank DDBJ	X14436 Genomic DNA. Translation: CAA32603.1. U28377 Genomic DNA. Translation: AAA69094.1. U00096 Genomic DNA. Translation: AAC75964.1. AP009048 Genomic DNA. Translation: BAE76991.1.
PIR	DEECGB. S04732.
RefSeq	AP_003485.1. NP_417402.1.
3D structure databases
SMR	P0A9B6. Positions 2-337.
ModBase	Search...
Protein-protein interaction databases
IntAct	P0A9B6. 1 interaction.
STRING	P0A9B6.
Proteomic databases
PRIDE	P0A9B6.
Genome annotation databases
GeneID	947413.
GenomeReviews	Gene locus JW2894 in contig AP009048_GR. Gene locus b2927 in contig U00096_GR.
KEGG	ecj:JW2894. eco:b2927.
Organism-specific databases
EchoBASE	EB0363.
EcoGene	EG10368. epd.
CMR	Search...
Phylogenomic databases
eggNOG	COG0057.
HOGENOM	HBG571736.
OMA	IQAKAVR.
Enzyme and pathway databases
BioCyc	EcoCyc:ERYTH4PDEHYDROG-MONOMER. ECOL168927:B2927-MONOMER. MetaCyc:ERYTH4PDEHYDROG-MONOMER.
Gene expression databases
Genevestigator	P0A9B6.
Family and domain databases
HAMAP	MF_01640. E4P_dehydrog. [Tree]
InterPro	IPR006422. E4P_DH_bac. IPR020830. GlycerAld_3-P_DH_AS. IPR020829. GlycerAld_3-P_DH_cat. IPR020832. GlycerAld_3-P_DH_cat_sub. IPR020831. GlycerAld_3-P_DH_family. IPR020828. GlycerAld_3-P_DH_NAD(P)_bd. IPR000173. GlycerAld_3-P_DH_subfam. IPR016040. NAD(P)-bd_dom. [Graphical view]
Gene3D	G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.
PANTHER	PTHR10836. GAP_DH. 1 hit.
Pfam	PF02800. Gp_dh_C. 1 hit. PF00044. Gp_dh_N. 1 hit. [Graphical view]
PIRSF	PIRSF000149. GAP_DH. 1 hit.
PRINTS	PR00078. G3PDHDRGNASE.
SMART	SM00846. Gp_dh_N. 1 hit. [Graphical view]
TIGRFAMs	TIGR01532. E4PD_g-proteo. 1 hit.
PROSITE	PS00071. GAPDH. 1 hit. [Graphical view]
ProtoNet	Search...

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Entry information

Entry name

E4PD_ECOLI

Accession

Primary (citable) accession number: P0A9B6
Secondary accession number(s): P11603, Q2M9R5

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2005
Last sequence update:	January 23, 2007
Last modified:	February 9, 2010
This is version 47 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents