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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	epd
Gene Synonym(s)	ECK2923, b2927, JW2894, gapB, gap2^[1]^[2]
Product Desc.	Epd^[2]^[3]; Component of erythrose 4-phosphate dehydrogenase^[2]^[3] Erythrose-4-P dehydrogenase^[4]
Product Synonyms(s)	D-erythrose 4-phosphate dehydrogenase^[1], B2927^[2]^[1], Epd^[2]^[1], GapB^[2]^[1], Gap2^[2]^[1] , ECK2923, gapB, JW2894, b2927
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): epd-pgk-fbaA^[2], epd-pgk^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	epd
Mnemonic	Erythrose-4-P dehydrogenase
Synonyms	ECK2923, b2927, JW2894, gapB, gap2^[1]^[2]
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	66.18 minutes	MG1655: 3071713..3070694 <gbrowseImage> name=NC_000913:3070694..3071713 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2959442..2958423 <gbrowseImage> name=NC_012967:2958423..2959442 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2957842..2958861 <gbrowseImage> name=NC_012759:2957842..2958861 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3072347..3071328 <gbrowseImage> name=NC_007779:3071328..3072347 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3165583..3164564 <gbrowseImage> name=NC_010473:3164564..3165583 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	3070697	Edman degradation	PMID:7751290
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Description	Reference	Availability	Comments
Δepd (Keio:JW2894)	deletion	deletion		PMID:16738554	Shigen
epd::Tn5KAN-I-SceI (FB20979)	Insertion at nt 643 in Plus orientation			PMID:15262929	E. coli Genome Project:FB20979	contains pKD46
epd::Tn5KAN-I-SceI (FB20980)	Insertion at nt 643 in Plus orientation			PMID:15262929	E. coli Genome Project:FB20980	does not contain pKD46
epdC155A,G,V		C155A,G,V	No significant activity			seeded from UniProt:P0A9B6
epdH182N		H182N	10-fold reduction in activity. Increases affinity for D-erythrose-4- phosphate and reduces affinity for glyceraldehyde 3-phosphate			seeded from UniProt:P0A9B6
epdC316A,Y		C316A,Y	Reduces activity and affinity for D-erythrose-4-phosphate and increases affinity for glyceraldehyde 3-phosphate			seeded from UniProt:P0A9B6
Δepd-11::Ery				PMID:9260967	CGSC:60142
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW2894	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCGTACGCGTAGCGATAAA Primer 2:CCtCTGAAAGCAACAGTAGCCAT
6C5	Kohara Phage	Genobase	PMID:3038334
1H10	Kohara Phage	Genobase	PMID:3038334
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[5]	est. P1 cotransduction: % ^[6]
speA210::Tn10	Linked marker	CAG12168 = CGSC7431^[5]	est. P1 cotransduction: 60% ^[6] Synonyms:zgd-210::Tn10, zgf-210::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10368	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10368	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000361	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947413	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0363	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009607	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	Epd
Synonyms	D-erythrose 4-phosphate dehydrogenase^[1], B2927^[2]^[1], Epd^[2]^[1], GapB^[2]^[1], Gap2^[2]^[1] , ECK2923, gapB, JW2894, b2927
Product description	Epd^[2]^[3]; Component of erythrose 4-phosphate dehydrogenase^[2]^[3] Erythrose-4-P dehydrogenase^[4]
EC number (for enzymes)	1.2.1.9^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004365	glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000173	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01640	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006422	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006006	glucose metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000173	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008615	pyridoxine biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01640	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008615	pyridoxine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0664	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042823	pyridoxal phosphate biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01640	P	Seeded from EcoCyc (v14.0)	complete
	GO:0042823	pyridoxal phosphate biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006422	P	Seeded from EcoCyc (v14.0)	complete
	GO:0048001	erythrose-4-phosphate dehydrogenase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01640	F	Seeded from EcoCyc (v14.0)	complete
	GO:0048001	erythrose-4-phosphate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006422	F	Seeded from EcoCyc (v14.0)	complete
	GO:0048001	erythrose-4-phosphate dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.2.1.72	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000173	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006422	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000173	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006422	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of erythrose 4-phosphate dehydrogenase	could be indirect
Protein	groL		PMID:16606699	Experiment(s):EBI-1144324
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc 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
Length	339
Mol. Wt	37.298 kDa
pI	6.7 (calculated)
Extinction coefficient	32,430 - 32,930 (calc based on 7 Y, 4 W, and 4 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Initiator Methionine	1	Removed	UniProt:P0A9B6
Domain	3..155	PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain		PMID:19920124
Domain	160..316	PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=epd taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130828	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947413	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009607	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A9B6	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10368	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10368	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947413	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000361	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0363	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MC4100	1.53E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	645	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	266	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	521	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
epd-pgk-fbaA
epd-pgk
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3071693..3071733 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2927 (EcoliWiki Page)	NCBI GEO profiles for epd
microarray	GenExpDB:b2927 (EcoliWiki Page)	Summary of data for epd from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to epd Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10368	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0363	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2927
EcoGene	EcoGene:EG10368	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000361	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009607	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Shigella flexneri	EPD	From SHIGELLACYC
E. coli O157	EPD	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
Pfam (EcoliWiki Page)	PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Panther (EcoliWiki Page)	PTHR10836:SF24
Superfamily (EcoliWiki Page)	SUPERFAMILY:55347
EcoCyc	EcoCyc:EG10368	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10368	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000361	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0363	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009607	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 ^2.13 ^2.14 ^2.15 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

epd:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to epd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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