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dapD:On One Page

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Standard Name

dapD

Gene Synonym(s)

ECK0164, b0166, JW0161, ssa[1]

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]

Function from GO

Cellular Component

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dapD[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(dapD)    Textpresso(dapD)

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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]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

3.99 minutes 

MG1655: 185947..185123
gbrowse_img.php?coord=185123..185947&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 188789..187965
gbrowse_img.php?coord=187965..188789&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 185947..185123
gbrowse_img.php?coord=185123..185947&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 160051..159227
gbrowse_img.php?coord=159227..160051&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 185122..185946
gbrowse_img.php?coord=185122..185946&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

dapD12::Mu

CGSC:11558

dapD8

CGSC:10283

dapD2

CGSC:11562

dapD4

CGSC:11564


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Notes

Genetic Resources

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

ResourceResource TypeSourceNotes/Reference

JW0161

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCAGCAGTTACAGAACATTAT

Primer 2:CCGTCGATGGTACGCAGCAGTTC

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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10207

EchoBASE (EcoliWiki Page)

EchoBASE:EB0203

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0166

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0201

EcoGene (EcoliWiki Page)

EcoGene:EG10207

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DAPD

CGSC (EcoliWiki Page)

CGSC:877

[url ENTREZ] (EcoliWiki Page)

ENTREZ:K02970

ASAP (EcoliWikiPage)

ASAP:ABE-0000565


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Notes

Links

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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]

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)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0005737

cytoplasm

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0008415

acyltransferase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR001451
SP_KW:KW-0012

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0019877

diaminopimelate biosynthetic process

GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

SP_KW:KW-0220
HAMAP:MF_00811

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0016757

transferase activity, transferring glycosyl groups

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005664

F

Seeded from EcoCyc [8]

complete

GO:0016740

transferase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR011004
SP_KW:KW-0808

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0008652

amino acid biosynthetic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0028

P

Seeded from EcoCyc [8]

complete

GO:0008666

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity

GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

EC:2.3.1.117
HAMAP:MF_00811

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0009085

lysine biosynthetic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0457

P

Seeded from EcoCyc [8]

complete

GO:0009089

lysine biosynthetic process via diaminopimelate

GO_REF:0000002
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR005664
HAMAP:MF_00811

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0005737

cytoplasm

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc 12.5 [7]

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 TypePartnerNotesReferencesEvidence

Protein

Subunits of tetrahydrodipicolinate succinylase

could be indirect


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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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.

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

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:MONOMER0-2001

SwissModel (EcoliWiki Page)

SwissModel:P0A9D8

UniProt (EcoliWiki Page)

UniProt:P0A9D8

PFAM (EcoliWiki Page)

of PF00132 PFAM:4 of PF00132

RefSeq (EcoliWiki Page)

RefSeq:NP_414708


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Notes

Links

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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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

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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gbrowse_img.php?coord=185927..185967&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

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

TypeReferenceNotes

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 NameResource TypeDescriptionSourceNotes
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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10207

EchoBASE (EcoliWiki Page)

EchoBASE:EB0203

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0166

EcoGene (EcoliWiki Page)

EcoGene:EG10207

[url ENTREZ] (EcoliWiki Page)

ENTREZ:K02970


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Notes

Links

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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.

OrganismHomologs (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.

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

of PF00132 PFAM:4 of PF00132


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ 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. ↑ 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. ↑ 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. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70

Categories

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