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Gene |

Product(s) |

Expression|

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Standard Name	ydiB
Gene Synonym(s)	ECK1690, b1692, JW1682, ydiB'^[1]^[2]
Product Desc.	EG11234^[2]^[3] Quinate/shikimate dehydrogenase, NAD(P)-dependent^[4]
Product Synonyms(s)	quinate/shikimate 5-dehydrogenase, NAD(P)-binding^[1], B1692^[2]^[1], YdiB^[2]^[1] , ECK1690, JW1682, b1692
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydiN^[2]
Regulation/Activity
Quick Links
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Notes

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YdiB is paralogous to AroE. Low catalytic efficiency may indicate a different in vivo substrate.^[4]

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	ydiB
Mnemonic	Systematic nomenclature
Synonyms	ECK1690, b1692, JW1682, ydiB'^[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	38.19 minutes	MG1655: 1771813..1772679 <gbrowseImage> name=NC_000913:1771813..1772679 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1751055..1751921 <gbrowseImage> name=NC_012967:1751055..1751921 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1663872..1664738 <gbrowseImage> name=NC_012759:1663872..1664738 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1775503..1776369 <gbrowseImage> name=NC_007779:1775503..1776369 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1862384..1863250 <gbrowseImage> name=NC_010473:1862384..1863250 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
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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: Type	Phenotype: Description	Reference	Availability	Comments
ΔydiB (Keio:JW1682)	deletion	deletion			PMID:16738554	Shigen CGSC9425^[5]
ydiBT106A		T106A		Increases KM for quinate 2000-fold. Increases KM for shikimate 70-fold			seeded from UniProt:P0A6D5
ydiBN92A		N92A		Alters protein structure. Loss of activity			seeded from UniProt:P0A6D5
ydiBD107A		D107A		Loss of activity towards quinate. Increases KM for shikimate 20000-fold			seeded from UniProt:P0A6D5
ydiBK71A		K71A		Increases KM for quinate 3200-fold. Increases KM for shikimate 170-fold			seeded from UniProt:P0A6D5
ydiBS67A		S67A		Reduces activity towards quinate about 6-fold			seeded from UniProt:P0A6D5
ΔydiB::kan	deletion		Biolog:respiration	unable to respire N-Acetyl-D-glucosamine	PMID:16095938
ΔydiB::kan	deletion		Biolog:respiration	unable to respire a-D-Glucose-1-phosphate	PMID:16095938
ΔydiB::kan	deletion		Biolog:respiration	unable to respire a-D-Glucose-6-phosphate	PMID:16095938
ΔydiB::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔydiB766::kan					PMID:16738554	CGSC:104314
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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
JW1682	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGATGTTACCGCAAAATACGA Primer 2:CCGGCACCGAACCCCATGACCTG
15G10	Kohara Phage	Genobase	PMID:3038334
8G8	Kohara Phage	Genobase	PMID:3038334
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[5]	est. P1 cotransduction: % ^[6] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: 84% ^[6] Synonyms:zdh-925::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:EG11234	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11234	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001212	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946200	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1216	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005651	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	YdiB
Synonyms	quinate/shikimate 5-dehydrogenase, NAD(P)-binding^[1], B1692^[2]^[1], YdiB^[2]^[1] , ECK1690, JW1682, b1692
Product description	EG11234^[2]^[3] Quinate/shikimate dehydrogenase, NAD(P)-dependent^[4]
EC number (for enzymes)	1.1.1.25^[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:0004764	shikimate 5-dehydrogenase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01578	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004764	shikimate 5-dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006151	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006151	C	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:0008652	cellular amino acid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0028	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009073	aromatic amino acid family biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01578	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009073	aromatic amino acid family biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0057	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030266	quinate 5-dehydrogenase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01578	F	Seeded from EcoCyc (v14.0)	complete
	GO:0033706	quinate/shikimate dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.282	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006151	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	References	Evidence
Protein	yggG	PMID:15690043	Experiment(s):EBI-887746
Protein	hemE	PMID:16606699	Experiment(s):EBI-1140506
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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 MDVTAKYELI GLMAYPIRHS LSPEMQNKAL EKAGLPFTYM AFEVDNDSFP GAIEGLKALK MRGTGVSMPN KQLACEYVDE LTPAAKLVGA INTIVNDDGY LRGYNTDGTG HIRAIKESGF DIKGKTMVLL GAGGASTAIG AQGAIEGLKE IKLFNRRDEF FDKALAFAQR VNENTDCVVT VTDLADQQAF AEALASADIL TNGTKVGMKP LENESLVNDI SLLHPGLLVT ECVYNPHMTK LLQQAQQAGC KTIDGYGMLL WQGAEQFTLW TGKDFPLEYV KQVMGFGA
Length	288
Mol. Wt	31.228 kDa
pI	4.9 (calculated)
Extinction coefficient	24,410 - 24,910 (calc based on 9 Y, 2 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	References
Domain	114..230	PF01488 Shikimate / quinate 5-dehydrogenase	PMID:19920124
Domain	12..94	PF08501 Shikimate dehydrogenase substrate binding 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=ydiB 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:16129648	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946200	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005651	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A6D5	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11234	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11234	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946200	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001212	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1216	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	Notes	Reference(s)
Protein	Ecoli K-12	0.364+/-0.028	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.012124711	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	12^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	8	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	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
ydiN
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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_000913:1771793..1771833 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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:b1692 (EcoliWiki Page)	NCBI GEO profiles for ydiB
microarray	GenExpDB:b1692 (EcoliWiki Page)	Summary of data for ydiB 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 ydiB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11234	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1216	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1692
EcoGene	EcoGene:EG11234	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001212	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005651	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
Arabidopsis thaliana	AT3G06350 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5ZCV1 (score: 1.000; bootstrap: 100%) Q5ZCU7 (score: 0.914)	From Inparanoid:20070104
Shigella flexneri	YDIB	From SHIGELLACYC
E. coli O157	YDIB	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Superfamily (EcoliWiki Page)	SUPERFAMILY:53223
Pfam (EcoliWiki Page)	PF01488 Shikimate / quinate 5-dehydrogenase
Pfam (EcoliWiki Page)	PF08501 Shikimate dehydrogenase substrate binding domain
EcoCyc	EcoCyc:EG11234	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11234	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001212	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1216	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005651	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 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).

ydiB: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 ydiB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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