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Standard Name	dmlA
Gene Synonym(s)	yeaU, ECK1798, b1800, JW1789, ttuC^[1]
Product Desc.	predicted dehydrogenase^[2]; D-malate dehydrogenase (decarboxylating)^[3] D-malate oxidase, NAD-dependent; probable tartrate dehydrogenase^[4]
Product Synonyms(s)	predicted dehydrogenase^[1], B1800^[2]^[1], YeaU^[2]^[1], TtuC^[2]^[1] , ECK1798, JW1789, yeaU, b1800
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yeaU^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 39 (http://afmb.cnrs-mrs.fr/article171.html). YeaU is 77% identical to a characterized tartrate dehydrogenase from Pseudomonas putida (SP:Q51945); this P. putida enzyme also has D-malate oxidase activity (Karsten, 2002). The D-malate oxidase activity of YeaU has been confirmed (Reed, 2006), but the probable tartrate dehydrogenase activity has not been tested. Mutations in yeaT or dmlA block growth on D-malate (Reed, 2006). After four hours of Zn(II) stress, protein levels increased (Easton, 2006).^[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	dmlA
Mnemonic	Systematic nomenclature
Synonyms	yeaU, ECK1798, b1800, JW1789, ttuC^[1]
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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	40.52 minutes	MG1655: 1879936..1881021 <gbrowseImage> name=NC_000913:1879936..1881021 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1860490..1861575 <gbrowseImage> name=NC_012967:1860490..1861575 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1771995..1773080 <gbrowseImage> name=NC_012759:1771995..1773080 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1883626..1884711 <gbrowseImage> name=NC_007779:1883626..1884711 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1970507..1971592 <gbrowseImage> name=NC_010473:1970507..1971592 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)	Reference	Availability
ΔyeaU (Keio:JW1789)	deletion	deletion	PMID:16738554	Shigen CGSC9500^[5]
ΔyeaU725::kan			PMID:16738554	CGSC:104398
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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
JW1789	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATGAAAACGATGCGTATTGC Primer 2:CCACGCAAAATAATTTTGCAAAT
zea-225::Tn10	Linked marker	CAG18465 = CGSC7388^[5]	est. P1 cotransduction: 71% ^[6] Synonyms:zdj-225::Tn10
eda-51::Tn10	Linked marker	CAG18486 = CGSC7392^[5]	est. P1 cotransduction: 10% ^[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:G6986	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13507	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003573	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946319	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3280	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005991	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	DmlA
Synonyms	predicted dehydrogenase^[1], B1800^[2]^[1], YeaU^[2]^[1], TtuC^[2]^[1] , ECK1798, JW1789, yeaU, b1800
Product description	predicted dehydrogenase^[2]; D-malate dehydrogenase (decarboxylating)^[3] D-malate oxidase, NAD-dependent; probable tartrate dehydrogenase^[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:0000287	magnesium ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001804	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019818	F	Seeded from EcoCyc (v14.0)	complete
	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:0009027	tartrate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011829	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009027	tartrate dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.93	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046553	D-malate dehydrogenase (decarboxylating) activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.83	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050319	tartrate decarboxylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.1.73	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001804	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011829	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019818	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011829	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019818	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	tufA	PMID:15690043	Experiment(s):EBI-881591
Protein	groL	PMID:16606699	Experiment(s):EBI-1140867
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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 MMKTMRIAAI PGDGIGKEVL PEGIRVLQAA AERWGFALSF EQMEWASCEY YSHHGKMMPD DWHEQLSRFD AIYFGAVGWP DTVPDHISLW GSLLKFRREF DQYVNLRPVR LFPGVPCPLA GKQPGDIDFY VVRENTEGEY SSLGGRVNEG TEHEVVIQES VFTRRGVDRI LRYAFELAQS RPRKTLTSAT KSNGLAISMP YWDERVEAMA ENYPEIRWDK QHIDILCARF VMQPERFDVV VASNLFGDIL SDLGPACTGT IGIAPSANLN PERTFPSLFE PVHGSAPDIY GKNIANPIAT IWAGAMMLDF LGNGDERFQQ AHNGILAAIE EVIAHGPKTP DMKGNATTPQ VADAICKIIL R
Length	361
Mol. Wt	40.315 kDa
pI	5.3 (calculated)
Extinction coefficient	58,900 - 59,525 (calc based on 10 Y, 8 W, and 5 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	6..355	PF00180 Isocitrate/isopropylmalate 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=yeaU 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:16129754	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946319	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005991	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76251	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6986	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13507	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946319	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003573	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3280	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	E. coli K-12 MG1655	46	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	49	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	29^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)
yeaU
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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_000913:1879916..1879956 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:b1800 (EcoliWiki Page)	NCBI GEO profiles for yeaU
microarray	GenExpDB:b1800 (EcoliWiki Page)	Summary of data for yeaU 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 (1879780..1880011) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ03; Well:A6^[7]
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Notes

Accessions Related to dmlA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6986	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3280	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1800
EcoGene	EcoGene:EG13507	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003573	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005991	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
Caenorhabditis briggsae	WBGene00036287 (score: 1.000; bootstrap: 100%) WBGene00026699 (score: 0.257) WBGene00037537 (score: 0.253)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00007993 (score: 1.000; bootstrap: 100%) WBGene00016266 (score: 0.262) WBGene00009440 (score: 0.252)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000015535 (score: 1.000; bootstrap: 100%) ENSMMUP00000028091 (score: 0.212)	From Inparanoid:20070104
Saccharomyces cerevisiae	YIL094C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC31G54 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	YEAU	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)	PF00180 Isocitrate/isopropylmalate dehydrogenase
Panther (EcoliWiki Page)	PTHR11835:SF8
Superfamily (EcoliWiki Page)	SUPERFAMILY:53659
EcoCyc	EcoCyc:G6986	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13507	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003573	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3280	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005991	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 ^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

dmlA: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 dmlA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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