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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	dmsD
Gene Synonym(s)	ECK1586, b1591, JW5262, ynfI^[1], ynfI
Product Desc.	DMS reductase maturation protein^[2]^[3] Redox enzyme maturation protein (REMP) for DmsA; twin-arginine leader-binding protein; binds DmsA and TorA TAT signal peptides; required for anaerobic growth on glycerol-DMSO medium; stimulates growth on glycerol-fumarate^[4]
Product Synonyms(s)	twin-argninine leader-binding protein for DmsA and TorA^[1], DmsD^[2]^[1], B1591^[2]^[1], YnfI^[2]^[1] , ECK1586, JW5262, ynfI, b1591
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ynfEFGH-dmsD^[2], ynfEFGHI
Regulation/Activity
Quick Links
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Notes

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dmsD is the fifth gene in the dmsABC-like operon ynfEFGH-dmsD. torD, dmsD and ycdY are paralogs.Overexpressed YdcY and DmsD interfere with apoTorA maturation by TorD, independent of the TorA signal peptide (Ilbert, 2004). DmsD may assist in DmsAB co-factor insertion. DmsD interacts with TatBC.^[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	dmsD
Mnemonic	DMSO reductase
Synonyms	ECK1586, b1591, JW5262, ynfI^[1], ynfI
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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	35.83 minutes	MG1655: 1662530..1663144 <gbrowseImage> name=NC_000913:1662530..1663144 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 1554589..1555203 <gbrowseImage> name=NC_012759:1554589..1555203 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1666220..1666834 <gbrowseImage> name=NC_007779:1666220..1666834 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1753491..1754105 <gbrowseImage> name=NC_010473:1753491..1754105 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	1662533	Edman degradation	PMID:11309116
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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
dmsD(del) (Keio:JW5262)	deletion	deletion			PMID:16738554	Shigen
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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
JW5262	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCCATTTTTCACAGCAAGA Primer 2:CCTCGAAACAGCGGTTTAACCGC
6F6	Kohara Phage	Genobase	PMID:3038334
E3F2	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: % ^[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:G6849	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13847	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003438	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945987	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3608	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005314	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	DmsD
Synonyms	twin-argninine leader-binding protein for DmsA and TorA^[1], DmsD^[2]^[1], B1591^[2]^[1], YnfI^[2]^[1] , ECK1586, JW5262, ynfI, b1591
Product description	DMS reductase maturation protein^[2]^[3] Redox enzyme maturation protein (REMP) for DmsA; twin-arginine leader-binding protein; binds DmsA and TorA TAT signal peptides; required for anaerobic growth on glycerol-DMSO medium; stimulates growth on glycerol-fumarate^[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:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008940	nitrate reductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003765	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009325	nitrate reductase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003765	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	C	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003765	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	rpmB	PMID:19402753	LCMS(ID Probability):99.6
Protein	ynfF	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):28.673484
Protein	dmsA	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):28.832391
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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 MLGMTHFSQQ DNFSVAARVL GALFYYAPES AEAAPLVAVL TSDGWETQWP LPEASLAPLV TAFQTQCEET HAQAWQRLFV GPWALPSPPW GSVWLDRESV LFGDSTLALR QWMREKGIQF EMKQNEPEDH FGSLLLMAAW LAENGRQTEC EELLAWHLFP WSTRFLDVFI EKAEHPFYRA LGELARLTLA QWQSQLLIPV AVKPLFR
Length	207
Mol. Wt	23.645 kDa
pI	4.8 (calculated)
Extinction coefficient	64,970 - 65,220 (calc based on 3 Y, 11 W, and 2 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:P69853
Domain	19..166	PF02613 Nitrate reductase delta subunit		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=dmsD taxon=562,83333 </beststructure>

Models

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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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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:90111302	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945987	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005314	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P69853	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6849	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13847	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945987	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003438	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3608	Escherichia coli str. K-12 substr. MG1655
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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 MG1655	663	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	210	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	314	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)
ynfEFGH-dmsD
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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_000913:1662510..1662550 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:b1591 (EcoliWiki Page)	NCBI GEO profiles for dmsD
microarray	GenExpDB:b1591 (EcoliWiki Page)	Summary of data for dmsD 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 dmsD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6849	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3608	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1591
EcoGene	EcoGene:EG13847	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003438	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005314	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	S1744	From SHIGELLACYC
E. coli O157	Z2581	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)	PF02613 Nitrate reductase delta subunit
Superfamily (EcoliWiki Page)	SUPERFAMILY:89155
EcoCyc	EcoCyc:G6849	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13847	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003438	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3608	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005314	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 ^1.9 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 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).

dmsD: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 dmsD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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