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Gene |

Product(s) |

Expression|

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Standard Name	dapD
Gene Synonym(s)	ECK0164, b0166, JW0161, ssa^[1], ssa
Product Desc.	tetrahydrodipicolinate succinylase subunit^[2]^[3]; Component of tetrahydrodipicolinate succinylase^[3] 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase; mutations suppress growth defects of strains lacking superoxide dismutase^[4]
Product Synonyms(s)	2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase^[1], B0166^[2]^[1], Ssa^[2]^[1], DapD^[2]^[1] , ECK0164, JW0161, ssa, b0166
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dapD^[2]
Regulation/Activity
Quick Links
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Notes

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A dapD 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; dapD is not an essential gene (Baba, 2006). DapD contains hexapeptide repeats. Binds TrxA (Kumar, 2004). HT_Cmplx35_Cyt: DapD+SpeB.^[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	dapD
Mnemonic	DiAminoPimelate
Synonyms	ECK0164, b0166, JW0161, ssa^[1], ssa
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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	3.99 minutes	MG1655: 185947..185123 <gbrowseImage> name=NC_000913:185123..185947 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 188789..187965 <gbrowseImage> name=NC_012967:187965..188789 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 185122..185946 <gbrowseImage> name=NC_012759:185122..185946 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 185947..185123 <gbrowseImage> name=NC_007779:185123..185947 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 160051..159227 <gbrowseImage> name=NC_010473:159227..160051 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	185123	Edman degradation	PMID:8740179 PMID:9298646
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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
dapD12::Mu						CGSC:11558
dapD8						CGSC:10283
dapD2						CGSC:11562
dapD4						CGSC:11564
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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
JW0161	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAGCAGTTACAGAACATTAT Primer 2:CCGTCGATGGTACGCAGCAGTTC
4E4	Kohara Phage	Genobase	PMID:3038334
21C8	Kohara Phage	Genobase	PMID:3038334
12D5	Kohara Phage	Genobase	PMID:3038334
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 22% ^[6]
yafC502::Tn10	Linked marker	CAG18436 = CGSC7328^[5]	est. P1 cotransduction: 12% ^[6] Synonyms:zae-502::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:EG10207	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10207	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944862	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000201	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0203	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000565	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	DapD
Synonyms	2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase^[1], B0166^[2]^[1], Ssa^[2]^[1], DapD^[2]^[1] , ECK0164, JW0161, ssa, b0166
Product description	tetrahydrodipicolinate succinylase subunit^[2]^[3]; Component of tetrahydrodipicolinate succinylase^[3] 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase; mutations suppress growth defects of strains lacking superoxide dismutase^[4]
EC number (for enzymes)	2.3.1.117^[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:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00811	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005664	C	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:0008415	acyltransferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0012	F	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:0008666	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00811	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008666	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005664	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008666	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.3.1.117	F	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:0009089	lysine biosynthetic process via diaminopimelate	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00811	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009089	lysine biosynthetic process via diaminopimelate	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005664	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011004	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018357	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019877	diaminopimelate biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00811	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 tetrahydrodipicolinate succinylase	could be indirect
Protein	dnaN		PMID:19402753	LCMS(ID Probability):99.6
Protein	hdeB		PMID:19402753	LCMS(ID Probability):99.6
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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 MQQLQNIIET AFERRAEITP ANADTVTREA VNQVIALLDS GALRVAEKID GQWVTHQWLK KAVLLSFRIN DNQVIEGAES RYFDKVPMKF ADYDEARFQK EGFRVVPPAA VRQGAFIARN TVLMPSYVNI GAYVDEGTMV DTWATVGSCA QIGKNVHLSG GVGIGGVLEP LQANPTIIED NCFIGARSEV VEGVIVEEGS VISMGVYIGQ STRIYDRETG EIHYGRVPAG SVVVSGNLPS KDGKYSLYCA VIVKKVDAKT RGKVGINELL RTID
Length	274
Mol. Wt	29.891 kDa
pI	5.6 (calculated)
Extinction coefficient	29,910 - 30,285 (calc based on 9 Y, 3 W, and 3 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
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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=dapD 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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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:16128159	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944862	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000565	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A9D8	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10207	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10207	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944862	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000201	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0203	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	1.25E+04	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 EMG2	420	molecules/cell	Medium: MOPS glucose minimal Temperature (°C): 37 Doubling time (min): Growth phase: Exponential OD: OD600 = 0.2 to 0.25 other: aerated	Quantitative protein sequencing	Spot ID: Ml04	PMID: 9298646
Protein	E. coli K-12 MG1655	15404	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	8536	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	11067	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)
dapD
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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_000913:185927..185967 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:b0166 (EcoliWiki Page)	NCBI GEO profiles for dapD
microarray	GenExpDB:b0166 (EcoliWiki Page)	Summary of data for dapD 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 dapD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10207	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0203	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0166
EcoGene	EcoGene:EG10207	Escherichia coli str. K-12 substr. MG1655
[url ENTREZ] (EcoliWiki Page)	ENTREZ:K02970
RegulonDB	RegulonDB:ECK120000201	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000565	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	DAPD	From SHIGELLACYC
E. coli O157	DAPD	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:51161
Panther (EcoliWiki Page)	PTHR19136:SF52
EcoCyc	EcoCyc:EG10207	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10207	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000201	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0203	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000565	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 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).

dapD: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 dapD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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