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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	ldhA
Gene Synonym(s)	ECK1377, b1380, JW1375, hslF, hslI, htpH^[1], htpH
Product Desc.	D-lactate dehydrogenase, NAD-dependent^[2]
Product Synonyms(s)	fermentative D-lactate dehydrogenase, NAD-dependent^[1], B1380^[3]^[1], HtpH^[3]^[1], HslI^[3]^[1], HslF^[3]^[1], LdhA^[3]^[1], HslF^[4], HslI^[4], ECK1377, hslF, hslI, htpH, JW1375, b1380
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ldhA^[3]
Regulation/Activity
Quick Links
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Notes

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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	ldhA
Mnemonic	Lactate dehydrogenase
Synonyms	ECK1377, b1380, JW1375, hslF, hslI, htpH^[1], htpH
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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	31.03 minutes	MG1655: 1440867..1439878 <gbrowseImage> name=NC_000913:1439878..1440867 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1434449..1433460 <gbrowseImage> name=NC_012967:1433460..1434449 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1331937..1332926 <gbrowseImage> name=NC_012759:1331937..1332926 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1444557..1443568 <gbrowseImage> name=NC_007779:1443568..1444557 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1531462..1530473 <gbrowseImage> name=NC_010473:1530473..1531462 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	Comments
ΔldhA (Keio:JW1375)	deletion	deletion	PMID:16738554	Shigen CGSC9216^[5]
ldhA::Tn5KAN-2 (FB20302)	Insertion at nt 612 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20302	contains pKD46
ldhA9				CGSC:34288
ldhA20::kan				CGSC:70512
ΔldhA744::kan			PMID:16738554	CGSC:101644
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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
JW1375	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAACTCGCCGTTTATAGCAC Primer 2:CCAACCAGTTCGTTCGGGCAGGT
4E7	Kohara Phage	Genobase	PMID:3038334
1E7	Kohara Phage	Genobase	PMID:3038334
zhj-3076::Tn10	Linked marker	CAG18640 = CGSC7453^[5]	est. P1 cotransduction: 81% ^[6]
trg-2::Tn10	Linked marker	CAG12026 = CGSC7376^[5]	est. P1 cotransduction: 7% ^[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:G592	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13186	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002700	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946315	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2978	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004619	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	LdhA
Synonyms	fermentative D-lactate dehydrogenase, NAD-dependent^[1], B1380^[3]^[1], HtpH^[3]^[1], HslI^[3]^[1], HslF^[3]^[1], LdhA^[3]^[1], HslF^[4], HslI^[4], ECK1377, hslF, hslI, htpH, JW1375, b1380
Product description	D-lactate dehydrogenase, NAD-dependent^[2]
EC number (for enzymes)	1.1.1.28^[1]
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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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006950	response to stress	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0346	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006139	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008720	D-lactate dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.28	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006139	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006140	F	Seeded from EcoCyc (v14.0)	complete
	GO:0048037	cofactor binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006140	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006139	F	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
	GO:0009408	response to heat	PMID:8349564	IEP: Inferred from Expression Pattern		P	In this paper, the protein later identified as LdhA is called HslI.	complete
	GO:0070404	NADH binding	PMID:4297265	IDA: Inferred from Direct Assay		F	Table I	complete
	GO:0009408	response to heat	PMID:15757896	IEP: Inferred from Expression Pattern		P	Jiang et al.^[7] did not detect changes in the level of LdhA activity with temperature in anaerobic cultures.	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	nadE	PMID:16606699	Experiment(s):EBI-1139724
Protein	uvrY	PMID:16606699	Experiment(s):EBI-1139724
Protein	yfjJ	PMID:16606699	Experiment(s):EBI-1139724
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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 MKLAVYSTKQ YDKKYLQQVN ESFGFELEFF DFLLTEKTAK TANGCEAVCI FVNDDGSRPV LEELKKHGVK YIALRCAGFN NVDLDAAKEL GLKVVRVPAY DPEAVAEHAI GMMMTLNRRI HRAYQRTRDA NFSLEGLTGF TMYGKTAGVI GTGKIGVAML RILKGFGMRL LAFDPYPSAA ALELGVEYVD LPTLFSESDV ISLHCPLTPE NYHLLNEAAF EQMKNGVMIV NTSRGALIDS QAAIEALKNQ KIGSLGMDVY ENERDLFFED KSNDVIQDDV FRRLSACHNV LFTGHQAFLT AEALTSISQT TLQNLSNLEK GETCPNELV
Length	329
Mol. Wt	36.535 kDa
pI	5.2 (calculated)
Extinction coefficient	16,390 - 17,140 (calc based on 11 Y, 0 W, and 6 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	References
Domain	3..329	PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	PMID:19920124
Domain	110..297	PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain	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=ldhA taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

</protect>

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:16129341	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946315	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004619	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P52643	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G592	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13186	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946315	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002700	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2978	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	Reference(s)
Protein	E. coli K-12 MC4100	1.20E+03	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	E. coli K-12 MG1655	2583	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	998	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	1592	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)
ldhA
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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

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<protect><gbrowseImage> name=NC_000913:1440847..1440887 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

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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:b1380 (EcoliWiki Page)	NCBI GEO profiles for ldhA
microarray	GenExpDB:b1380 (EcoliWiki Page)	Summary of data for ldhA 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 (1440786..1441094) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ13; Well:A9^[8]
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Notes

Accessions Related to ldhA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G592	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2978	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1380
EcoGene	EcoGene:EG13186	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002700	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004619	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	ENSANGP00000017163 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000018739 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000004404 (score: 1.000; bootstrap: 100%) ENSBTAP00000004405 (score: 0.755)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00018642 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000024542 (score: 1.000; bootstrap: 100%) ENSCAFP00000018820 (score: 0.773)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000018698 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-010130-1 (score: 1.000; bootstrap: 98%) ZDB-CDNA-040425-193 (score: 1.000; bootstrap: 97%) ZDB-CDNA-040425-196 (score: 0.691) ZDB-CDNA-040425-195 (score: 0.691) ZDB-CDNA-040425-197 (score: 0.691) ZDB-CDNA-040425-194 (score: 0.689) ZDB-GENE-010130-2 (score: 0.640) ZDB-GENE-050902-1 (score: 0.633)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0204015 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0020496 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA20456-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000012349 (score: 1.000; bootstrap: 92%) ENSGALP00000015832 (score: 0.664) ENSGALP00000025299 (score: 0.509) ENSGALP00000021909 (score: 0.079)	From Inparanoid:20070104
Homo sapiens	ENSP00000290921 (score: 1.000; bootstrap: 100%) ENSP00000311825 (score: 0.787) ENSP00000352871 (score: 0.093)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000010915 (score: 1.000; bootstrap: 100%) ENSMMUP00000029015 (score: 0.796) ENSMMUP00000020190 (score: 0.545) ENSMMUP00000002072 (score: 0.516) ENSMMUP00000012072 (score: 0.409)	From Inparanoid:20070104
Mus musculus	MGI:1201685 (score: 1.000; bootstrap: 100%) MGI:1201686 (score: 0.784)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000035064 (score: 1.000; bootstrap: 100%) ENSRNOP00000023404 (score: 0.775) ENSRNOP00000051319 (score: 0.543)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC1867c (score: 1.000; bootstrap: 100%) SPAC1862c (score: 0.507)	From Inparanoid:20070104
Shigella flexneri	LDHA	From SHIGELLACYC
E. coli O157	LDHA	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)	PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
Pfam (EcoliWiki Page)	PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Superfamily (EcoliWiki Page)	SUPERFAMILY:52283
Panther (EcoliWiki Page)	PTHR10996:SF17
EcoCyc	EcoCyc:G592	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13186	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002700	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2978	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004619	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 ^1.14 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 ^4.3 Chuang, SE & Blattner, FR (1993) Characterization of twenty-six new heat shock genes of Escherichia coli. J. Bacteriol. 175 5242-52 PubMed
↑ ^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).
↑ Jiang, GR et al. (2001) Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli. Microbiology (Reading, Engl.) 147 2437-46 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ldhA: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 ldhA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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