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Gene |

Product(s) |

Expression|

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Standard Name	grxD
Gene Synonym(s)	ydhD, ECK1650, b1654, JW1646^[1]^[2], JW1646
Product Desc.	glutaredoxin 4^[2]^[3] Monothiol glutaredoxin Grx4, with CxxS motif; substrate for thioredoxin reductase; essential gene^[4]
Product Synonyms(s)	conserved protein^[1], B1654^[2]^[1], YdhD^[2]^[1], GrxD^[2]^[1], Grx4^[2]^[1] , ECK1650, JW1646, ydhD, b1654
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): grxD^[2]
Regulation/Activity
Quick Links
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Notes

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UPF0055 family. Highly abundant protein, induced during stationary phase or iron depletion. Not a substrate for glutathione reductase.^[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	grxD
Mnemonic	Glutaredoxin
Synonyms	ydhD, ECK1650, b1654, JW1646^[1]^[2], JW1646
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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	37.33 minutes, 37.33 minutes	MG1655: 1732125..1731778 <gbrowseImage> name=NC_000913:1731778..1732125 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 1623837..1624184 <gbrowseImage> name=NC_012759:1623837..1624184 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1735815..1735468 <gbrowseImage> name=NC_007779:1735468..1735815 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1822696..1822349 <gbrowseImage> name=NC_010473:1822349..1822696 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)	Reference	Availability	Comments
ydhD::Tn5KAN-I-SceI (FB20407)	Insertion at nt 227 in Plus orientation	PMID:15262929	E. coli Genome Project:FB20407	contains pKD46
ydhD::Tn5KAN-I-SceI (FB20408)	Insertion at nt 227 in Plus orientation	PMID:15262929	E. coli Genome Project:FB20408	does not contain pKD46
ΔgrxD732::kan		PMID:16738554	CGSC:106204
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
6F11	Kohara Phage	Genobase	PMID:3038334
4H6	Kohara Phage	Genobase	PMID:3038334
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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:EG12181	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12181	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002074	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946169	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2098	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005527	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	YdhD
Synonyms	conserved protein^[1], B1654^[2]^[1], YdhD^[2]^[1], GrxD^[2]^[1], Grx4^[2]^[1] , ECK1650, JW1646, ydhD, b1654
Product description	glutaredoxin 4^[2]^[3] Monothiol glutaredoxin Grx4, with CxxS motif; substrate for thioredoxin reductase; essential gene^[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: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:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002109	F	Seeded from EcoCyc (v14.0)	complete
	GO:0015035	protein disulfide oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002109	F	Seeded from EcoCyc (v14.0)	complete
	GO:0022900	electron transport chain	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0249	P	Seeded from EcoCyc (v14.0)	complete
	GO:0045454	cell redox homeostasis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002109	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	selD	PMID:16606699	Experiment(s):EBI-1140371
Protein	rplE	PMID:16606699	Experiment(s):EBI-1140371
Protein	nuoE	PMID:16606699	Experiment(s):EBI-1140371
Protein	rplB	PMID:16606699	Experiment(s):EBI-1140371
Protein	slyD	PMID:16606699	Experiment(s):EBI-1140371
Protein	cysQ	PMID:16606699	Experiment(s):EBI-1140371
Protein	nadE	PMID:16606699	Experiment(s):EBI-1140371
Protein	yeeT	PMID:16606699	Experiment(s):EBI-1140371
Protein	mreB	PMID:16606699	Experiment(s):EBI-1140371
Protein	nrdI	PMID:16606699	Experiment(s):EBI-1140371
Protein	rplO	PMID:16606699	Experiment(s):EBI-1140371
Protein	rpsC	PMID:16606699	Experiment(s):EBI-1140371
Protein	rpsB	PMID:16606699	Experiment(s):EBI-1140371
Protein	fur	PMID:16606699	Experiment(s):EBI-1140371
Protein	napC	PMID:16606699	Experiment(s):EBI-1140371
Protein	csrA	PMID:16606699	Experiment(s):EBI-1140371
Protein	rpsD	PMID:16606699	Experiment(s):EBI-1140371
Protein	bolA	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):9.486753
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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 MSTTIEKIQR QIAENPILLY MKGSPKLPSC GFSAQAVQAL AACGERFAYV DILQNPDIRA ELPKYANWPT FPQLWVDGEL VGGCDIVIEM YQRGELQQLI KETAAKYKSE EPDAE
Length	115
Mol. Wt	12.878 kDa
pI	4.5 (calculated)
Extinction coefficient	18,450 - 18,825 (calc based on 5 Y, 2 W, and 3 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	17..81	PF00462 Glutaredoxin		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=grxD 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:16129612	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946169	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005527	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AC69	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12181	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12181	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946169	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002074	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2098	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	448.401+/-1.966	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.11538+/-0.00952	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.390489914	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	20731	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	8964	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	8373	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)
grxD
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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_000913:1732105..1732145 source=MG1655 flip=1 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:b1654 (EcoliWiki Page)	NCBI GEO profiles for grxD
microarray	GenExpDB:b1654 (EcoliWiki Page)	Summary of data for grxD 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
	GFP Fusion	Intergenic region (1732025..1732518) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:D4^[5]
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Notes

Accessions Related to grxD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12181	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2098	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1654
EcoGene	EcoGene:EG12181	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002074	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005527	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
Anopheles gambiae	ENSANGP00000022155 (score: 1.000; bootstrap: 100%) ENSANGP00000015021 (score: 0.087)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000026693 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT4G04950 (score: 1.000; bootstrap: 56%) AT4G32580 (score: 0.217)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000017860 (score: 1.000; bootstrap: 100%) ENSBTAP00000038450 (score: 0.285)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00040544 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00017062 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000019565 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000003944 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-041010-22 (score: 1.000; bootstrap: 100%) ZDB-CDNA-041010-22 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0203208 (score: 1.000; bootstrap: 66%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0030584 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA12959-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000018029 (score: 1.000; bootstrap: 77%)	From Inparanoid:20070104
Homo sapiens	ENSP00000328570 (score: 1.000; bootstrap: 68%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000022473 (score: 1.000; bootstrap: 83%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000015835 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1920296 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5JM41 (score: 1.000; bootstrap: 52%) Q5VR05 (score: 1.000; bootstrap: 51%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000011409 (score: 1.000; bootstrap: 92%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000005781 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YPL059W (score: 1.000; bootstrap: 70%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAPB2B42 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000145294 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00021940001 (score: 1.000; bootstrap: 77%) GSTENP00011267001 (score: 0.279)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000024680 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YDHD	From SHIGELLACYC
E. coli O157	YDHD	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00462 Glutaredoxin
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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 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 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.
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

grxD: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 grxD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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