{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	menD
Gene Synonym(s)	ECK2258, b2264, JW5374^[1], JW5374
Product Desc.	MEND^[2]^[3]; Component of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase^[3] SEPHCHC synthase, menaquinone biosynthesis^[4]
Product Synonyms(s)	bifunctional 2-oxoglutarate decarboxylase and SHCHC synthase^[1], B2264^[2]^[1], MenD^[2]^[1] , ECK2258, JW5374, b2264
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): menFD-yfbB-menBCE^[2]
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

Mistakenly thought to be SHCHC synthase (Jiang, 2007). SEPHCHC is 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic acid and SHCHC is 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate.^[4]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

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

Standard name	menD
Mnemonic	Menaquinone (vitamin K2)
Synonyms	ECK2258, b2264, JW5374^[1], JW5374
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	51.2 minutes	MG1655: 2377281..2375611 <gbrowseImage> name=NC_000913:2375611..2377281 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2325772..2324102 <gbrowseImage> name=NC_012967:2324102..2325772 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2261416..2263086 <gbrowseImage> name=NC_012759:2261416..2263086 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2383929..2382259 <gbrowseImage> name=NC_007779:2382259..2383929 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2468269..2466599 <gbrowseImage> name=NC_010473:2466599..2468269 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

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

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

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
ΔmenD (Keio:JW5374)	deletion	deletion		PMID:16738554	Shigen CGSC11349^[5]
menD::Tn5KAN-2 (FB20733)	Insertion at nt 234 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20733	does not contain pKD46
menD::Tn5KAN-2 (FB20734)	Insertion at nt 234 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20734	contains pKD46
menDE55Q		E55Q	Loss of activity			seeded from UniProt:P17109
ΔmenD746::kan				PMID:16738554	CGSC:101816
edit table

Notes

Genetic Interactions

[back to top]

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

</protect>

Notes

Genetic Resources

[back to top]

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

Resource	Resource Type	Source	Notes/Reference
JW5374	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCAGTAAGCGCATTTAACCG Primer 2:CCTAAATGGCTTACCTGCGCCAG
5H12	Kohara Phage	Genobase	PMID:3038334
9F11	Kohara Phage	Genobase	PMID:3038334
zfa-723::Tn10	Linked marker	CAG12178 gyrA+ = CGSC7526^[5]	est. P1 cotransduction: 27% ^[6] Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[5]	est. P1 cotransduction: 62% ^[6] Synonyms:zej-223::Tn10
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10579	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10579	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000572	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946720	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0574	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007482	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name	MenD
Synonyms	bifunctional 2-oxoglutarate decarboxylase and SHCHC synthase^[1], B2264^[2]^[1], MenD^[2]^[1] , ECK2258, JW5374, b2264
Product description	MEND^[2]^[3]; Component of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase^[3] SEPHCHC synthase, menaquinone biosynthesis^[4]
EC number (for enzymes)	4.1.1.71^[1] 2.5.1.64^[1]
edit table

Notes

Function

[back to top]

<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				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0000287	magnesium ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01659	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009234	menaquinone biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01659	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009234	menaquinone biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004433	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009234	menaquinone biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0474	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019142	2-hydroxyglutarate synthase activity	PMID:12952533	ISS: Inferred from Sequence or Structural Similarity		F	Seeded from EcoCyc (v14.0)	Missing: with/from
	GO:0030145	manganese ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01659	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030976	thiamin pyrophosphate binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01659	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030976	thiamin pyrophosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004433	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030976	thiamin pyrophosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011766	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030976	thiamin pyrophosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012001	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
	GO:0070204	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004433	F	Seeded from EcoCyc (v14.0)	complete
	GO:0070204	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.2.1.9	F	Seeded from EcoCyc (v14.0)	complete
edit table

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 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase	could be indirect
edit table

</protect>

Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MSVSAFNRRW AAVILEALTR HGVRHICIAP GSRSTPLTLA AAENSAFIHH THFDERGLGH LALGLAKVSK QPVAVIVTSG TAVANLYPAL IEAGLTGEKL ILLTADRPPE LIDCGANQAI RQPGMFASHP THSISLPRPT QDIPARWLVS TIDHALGTLH AGGVHINCPF AEPLYGEMDD TGLSWQQRLG DWWQDDKPWL REAPRLESEK QRDWFFWRQK RGVVVAGRMS AEEGKKVALW AQTLGWPLIG DVLSQTGQPL PCADLWLGNA KATSELQQAQ IVVQLGSSLT GKRLLQWQAS CEPEEYWIVD DIEGRLDPAH HRGRRLIANI ADWLELHPAE KRQPWCVEIP RLAEQAMQAV IARRDAFGEA QLAHRICDYL PEQGQLFVGN SLVVRLIDAL SQLPAGYPVY SNRGASGIDG LLSTAAGVQR ASGKPTLAIV GDLSALYDLN ALALLRQVSA PLVLIVVNNN GGQIFSLLPT PQSERERFYL MPQNVHFEHA AAMFELKYHR PQNWQELETA FADAWRTPTT TVIEMVVNDT DGAQTLQQLL AQVSHL
Length	556
Mol. Wt	61.367 kDa
pI	6.6 (calculated)
Extinction coefficient	106,910 - 107,785 (calc based on 9 Y, 17 W, and 7 C residues)
edit table

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	396..535	PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain	PMID:19920124
Domain	8..171	PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain	PMID:19920124
edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

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

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130199	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946720	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007482	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P17109	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10579	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10579	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946720	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000572	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0574	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MC4100	1.24E+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	9.335+/-0.049	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.018562874	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	166	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	44	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	62	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

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

Transcription unit(s)
menFD-yfbB-menBCE
edit table

Figure courtesy of RegulonDB

</protect>

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

[back to top]

<protect><gbrowseImage> name=NC_000913:2377261..2377301 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

</protect>

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

[back to top]

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

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2264 (EcoliWiki Page)	NCBI GEO profiles for menD
microarray	GenExpDB:b2264 (EcoliWiki Page)	Summary of data for menD from multiple microarray studies
edit table

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 (2377188..2377399) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:A9^[7]
edit table

Notes

Accessions Related to menD Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10579	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0574	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2264
EcoGene	EcoGene:EG10579	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000572	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007482	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

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

Organism	Homologs (Statistics)	Comments
Arabidopsis thaliana	AT1G68890 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	MEND	From SHIGELLACYC
E. coli O157	MEND	From ECOO157CYC
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:52518
Superfamily (EcoliWiki Page)	SUPERFAMILY:52518
Panther (EcoliWiki Page)	PTHR18968:SF3
Pfam (EcoliWiki Page)	PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
Pfam (EcoliWiki Page)	PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
EcoCyc	EcoCyc:EG10579	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10579	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000572	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0574	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007482	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

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 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 ^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 ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

menD:On One Page

Quickview

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 menD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search