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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	dapA
Gene Synonym(s)	ECK2474, b2478, JW2463^[1], JW2463
Product Desc.	DapA^[2]^[3]; Component of dihydrodipicolinate synthase^[2]^[3] Dihydrodipicolinate synthase^[4]
Product Synonyms(s)	dihydrodipicolinate synthase^[1], B2478^[2]^[1], DapA^[2]^[1] , ECK2474, JW2463, b2478
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dapA-nlpB^[2]
Regulation/Activity
Quick Links
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Notes

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DapA levels may be influenced by GroES and GroEL. A dapA mutant is not in the Keio collection; DAP auxotrophs require added DAP to grow and since no DAP was added during mutant construction, no auxotrophic mutants were recovered; dapA is not an essential gene (Baba, 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	dapA
Mnemonic	DiAminoPimelate
Synonyms	ECK2474, b2478, JW2463^[1], JW2463
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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	55.97 minutes	MG1655: 2597782..2596904 <gbrowseImage> name=NC_000913:2596904..2597782 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2520588..2519710 <gbrowseImage> name=NC_012967:2519710..2520588 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2482709..2483587 <gbrowseImage> name=NC_012759:2482709..2483587 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2598416..2597538 <gbrowseImage> name=NC_007779:2597538..2598416 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2689547..2688669 <gbrowseImage> name=NC_010473:2688669..2689547 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	2596904	Edman degradation	PMID:9298646 PMID:9600841 PMID:9740056
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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	AA change(s)	Phenotype: Description	Availability	Comments
dapAY107F	Y107F	Reduced Kcat by 90%		seeded from UniProt:P0A6L2
dapAY133F	Y133F	Reduced Kcat by 99.7%. Reduced affinity for both substrates		seeded from UniProt:P0A6L2
dapAR138A,H	R138A,H	Strongly increased KM for L- aspartate 4-semialdehyde. No effect on KM for pyruvate. Reduced activity by 99.7%		seeded from UniProt:P0A6L2
dapAT44V	T44V	Reduced Kcat by 99.9%		seeded from UniProt:P0A6L2
dapA15			CGSC:11566
dapA16			CGSC:11568
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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
JW2463	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTCACGGGAAGTATTGTCGC Primer 2:CCaAGCAAACCGGCATGCTTAAG
4C11	Kohara Phage	Genobase	PMID:3038334
5A8	Kohara Phage	Genobase	PMID:3038334
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 90% ^[6]
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 2% ^[6] Synonyms:zff-208::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:EG10205	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10205	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000199	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946952	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0201	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008163	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	DapA
Synonyms	dihydrodipicolinate synthase^[1], B2478^[2]^[1], DapA^[2]^[1] , ECK2474, JW2463, b2478
Product description	DapA^[2]^[3]; Component of dihydrodipicolinate synthase^[2]^[3] Dihydrodipicolinate synthase^[4]
EC number (for enzymes)	4.2.1.52^[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:0008840	dihydrodipicolinate synthase activity	PMID:4910051	IDA: Inferred from Direct Assay		F		complete
	GO:0019877	diaminopimelate biosynthetic process	PMID:4910051	IDA: Inferred from Direct Assay		P		complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013785	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002220	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013785	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020624	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020625	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008652	cellular amino acid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0028	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008840	dihydrodipicolinate synthase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00418	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008840	dihydrodipicolinate synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005263	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008840	dihydrodipicolinate synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.2.1.52	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009085	lysine biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00418	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009085	lysine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0457	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002220	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020624	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020625	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:0019877	diaminopimelate biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00418	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019877	diaminopimelate biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005263	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019877	diaminopimelate biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0220	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	Notes	References	Evidence
Protein	Subunits of dihydrodipicolinate synthase	could be indirect
Protein	nadE		PMID:16606699	Experiment(s):EBI-1142999
Protein	ycbB		PMID:16606699	Experiment(s):EBI-1142999
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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 MFTGSIVAIV TPMDEKGNVC RASLKKLIDY HVASGTSAIV SVGTTGESAT LNHDEHADVV MMTLDLADGR IPVIAGTGAN ATAEAISLTQ RFNDSGIVGC LTVTPYYNRP SQEGLYQHFK AIAEHTDLPQ ILYNVPSRTG CDLLPETVGR LAKVKNIIGI KEATGNLTRV NQIKELVSDD FVLLSGDDAS ALDFMQLGGH GVISVTANVA ARDMAQMCKL AAEGHFAEAR VINQRLMPLH NKLFVEPNPI PVKWACKELG LVATDTLRLP MTPITDSGRE TVRAALKHAG LL
Length	292
Mol. Wt	31.269 kDa
pI	6.4 (calculated)
Extinction coefficient	12,950 - 13,575 (calc based on 5 Y, 1 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	1..290	PF00701 Dihydrodipicolinate synthetase family		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=dapA taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16130403	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946952	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008163	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A6L2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10205	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10205	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946952	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000199	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0201	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 MC4100	1.19E+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	Ecoli K-12	1.106+/-0.05	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.328018223	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	4514	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	2172	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	2885	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)
dapA-nlpB
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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_000913:2597762..2597802 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

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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:b2478 (EcoliWiki Page)	NCBI GEO profiles for dapA
microarray	GenExpDB:b2478 (EcoliWiki Page)	Summary of data for dapA 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 (2597709..2597936) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:E11^[7]
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Notes

Accessions Related to dapA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10205	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0201	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2478
EcoGene	EcoGene:EG10205	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000199	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008163	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	ENSANGP00000000124 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000001626 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G60880 (score: 1.000; bootstrap: 100%) AT2G45440 (score: 0.861)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000004738 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-2242 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-3189 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000009883 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000026348 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	P24846 (score: 1.000; bootstrap: 100%) P24847 (score: 0.761) Q9LWB9 (score: 0.743) Q39535 (score: 0.720) P26259 (score: 0.717) Q7XM43 (score: 0.668) Q7XPB5 (score: 0.580)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000130055 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00009068001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000023509 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	DAPA	From SHIGELLACYC
E. coli O157	DAPA	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)	PF00701 Dihydrodipicolinate synthetase family
Superfamily (EcoliWiki Page)	SUPERFAMILY:51569
Panther (EcoliWiki Page)	PTHR12128:SF10
EcoCyc	EcoCyc:EG10205	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10205	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000199	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0201	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008163	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 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 ^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 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

dapA:On One Page

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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 dapA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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