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Gene |

Product(s) |

Expression|

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Standard Name	yqhD
Gene Synonym(s)	ECK3003, b3011, JW2978^[1], JW2978
Product Desc.	NADP-dependent alcohol dehydrogenase^[2]^[3] Aldehyde reductase, protects against lipid oxidation; NADPH-dependent; contains Zn; homodimer^[4]
Product Synonyms(s)	alcohol dehydrogenase, NAD(P)-dependent^[1], B3011^[2]^[1], YqhD^[2]^[1] , ECK3003, JW2978, b3011
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yqhD^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 57 (http://afmb.cnrs-mrs.fr/article171.html). HT_Cmplx40_Cyt: YbgI+YqhD. YqhD is induced under conditions that favor lipid oxidation; overexpression increases resistance to paraquat, hydrogen peroxide and the lipid peroxidation-derived aldehydes butanaldehyde, propanaldehyde, acrolein and malondialdehyde; yqhD mutants are senstive to paraquat and hydrogen peroxide (Perez, 2008). YqhD catalyzes the NADPH-dependent reduction of acetaldehyde, malondialdehyde, propanaldehyde, butanaldehyde and acrolein in vitro (Perez, 2008). YqhD was reported to have no aldehyde dehydrogenase activity and to have in vitro alcohol dehydrogenase activity with a preference for alcohols longer than C3(Sulzenbacher , 2004), however these results are contradicted by Perez (2009).^[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	yqhD
Mnemonic	Systematic nomenclature
Synonyms	ECK3003, b3011, JW2978^[1], JW2978
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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	67.97 minutes	MG1655: 3153377..3154540 <gbrowseImage> name=NC_000913:3153377..3154540 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3089527..3090690 <gbrowseImage> name=NC_012967:3089527..3090690 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3040525..3041688 <gbrowseImage> name=NC_012759:3040525..3041688 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3154011..3155174 <gbrowseImage> name=NC_007779:3154011..3155174 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3251122..3252285 <gbrowseImage> name=NC_010473:3251122..3252285 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
ΔyqhD (Keio:JW2978)	deletion	deletion			PMID:16738554	Shigen CGSC10288^[5]
ΔyqhD783::kan					PMID:16738554	CGSC:105986
pUC19-yqhD+	none, multicopy expression of yqhD+		Sensitivity to	increased sensitivity to propanal or butanal	PMID:22538653		Fig. 2
yqhD+ constitutive expression	none, constitutive expression due to mutations in gene for activator YqhC		Resistant to	resistant glyoxal and methylglyoxal	PMID:20543070		Fig. 3
yqhD(del)::kan			Sensitivity to	sensitive to glyoxal	PMID:20543070		Fig. 4, MG1655 strain background
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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
JW2978	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACAACTTTAATCTGCACAC Primer 2:CCGCGGGCGGCTTCGTATATACG
5C10	Kohara Phage	Genobase	PMID:3038334
6H4	Kohara Phage	Genobase	PMID:3038334
metC162::Tn10	Linked marker	CAG18475 = CGSC7435^[5]	est. P1 cotransduction: 90% ^[6]
tolC210::Tn10	Linked marker	CAG12184 = CGSC7437^[5]	est. P1 cotransduction: 39% ^[6]
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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:G7564	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13014	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004123	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947493	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2834	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009888	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	YqhD
Synonyms	alcohol dehydrogenase, NAD(P)-dependent^[1], B3011^[2]^[1], YqhD^[2]^[1] , ECK3003, JW2978, b3011
Product description	NADP-dependent alcohol dehydrogenase^[2]^[3] Aldehyde reductase, protects against lipid oxidation; NADPH-dependent; contains Zn; homodimer^[4]
EC number (for enzymes)
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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:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0018455

alcohol dehydrogenase [NAD(P)+] activity

PMID:15327949

IDA: Inferred from Direct Assay

F

Table 3

Zn found at active site in crystallized protein

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	glpD	PMID:16606699	Experiment(s):EBI-1144545
Protein	slyD	PMID:16606699	Experiment(s):EBI-1144545
Protein	gadB	PMID:19402753	LCMS(ID Probability):99.6
Protein	eno	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplS	PMID:19402753	LCMS(ID Probability):99.6
Protein	dnaN	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsF	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpoA	PMID:19402753	LCMS(ID Probability):99.5
Protein	dps	PMID:19402753	LCMS(ID Probability):99.6
Protein	cydA	PMID:19402753	LCMS(ID Probability):99.6
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Notes

Localization

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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 MNNFNLHTPT RILFGKGAIA GLREQIPHDA RVLITYGGGS VKKTGVLDQV LDALKGMDVL EFGGIEPNPA YETLMNAVKL VREQKVTFLL AVGGGSVLDG TKFIAAAANY PENIDPWHIL QTGGKEIKSA IPMGCVLTLP ATGSESNAGA VISRKTTGDK QAFHSAHVQP VFAVLDPVYT YTLPPRQVAN GVVDAFVHTV EQYVTKPVDA KIQDRFAEGI LLTLIEDGPK ALKEPENYDV RANVMWAATQ ALNGLIGAGV PQDWATHMLG HELTAMHGLD HAQTLAIVLP ALWNEKRDTK RAKLLQYAER VWNITEGSDD ERIDAAIAAT RNFFEQLGVP THLSDYGLDG SSIPALLKKL EEHGMTQLGE NHDITLDVSR RIYEAAR
Length	387
Mol. Wt	42.097 kDa
pI	6.1 (calculated)
Extinction coefficient	42,400 - 42,525 (calc based on 10 Y, 5 W, and 1 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
Domain	9..376	PF00465 Iron-containing alcohol dehydrogenase		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=yqhD 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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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:16130909	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947493	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009888	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q46856	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7564	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13014	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947493	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004123	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2834	Escherichia coli str. K-12 substr. MG1655
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Notes

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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	E. coli K-12 MC4100	6.13E+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	Ecoli K-12	5.143+/-0.16	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.003869304	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	783	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	309	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	445	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)
yqhD
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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_000913:3153357..3153397 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:b3011 (EcoliWiki Page)	NCBI GEO profiles for yqhD
microarray	GenExpDB:b3011 (EcoliWiki Page)	Summary of data for yqhD 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 yqhD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7564	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2834	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3011
EcoGene	EcoGene:EG13014	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004123	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009888	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	YQHD	From SHIGELLACYC
E. coli O157	YQHD	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)	PF00465 Iron-containing alcohol dehydrogenase
Superfamily (EcoliWiki Page)	SUPERFAMILY:56796
EcoCyc	EcoCyc:G7564	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13014	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004123	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2834	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009888	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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↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 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 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).

yqhD: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 yqhD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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