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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	dapE
Gene Synonym(s)	ECK2467, b2472, JW2456, msgB^[1], msgB
Product Desc.	N-succinyl-L-diaminopimelate desuccinylase subunit^[2]^[3]; Component of [[:Category:Complex:N-succinyl-L-diaminopimelate desuccinylase\|N-succinyl-L-diaminopimelate desuccinylase]]^[3] N-succinyl-diaminopimelate desuccinylase, DAP/lysine biosynthesis, contains Zn(2+)/Co(2+)^[4]
Product Synonyms(s)	N-succinyl-diaminopimelate deacylase^[1], MsgB^[2]^[1], B2472^[2]^[1], DapE^[2]^[1] , ECK2467, JW2456, msgB, b2472
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yffB^[2]
Regulation/Activity
Quick Links
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Notes

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A dapE 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; dapE is not an essential gene (Baba, 2006). dapE(msgB) is a multicopy suppressor of grpE(Ts). Salmonella DapE also has Zn(2+)/Mn(2+)-dependent Asp-X dipeptidase activity.^[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	dapE
Mnemonic	DiAminoPimelate
Synonyms	ECK2467, b2472, JW2456, msgB^[1], msgB
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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	55.81 minutes	MG1655: 2589629..2590756 <gbrowseImage> name=NC_000913:2589629..2590756 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2512435..2513562 <gbrowseImage> name=NC_012967:2512435..2513562 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2475434..2476561 <gbrowseImage> name=NC_012759:2475434..2476561 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2590263..2591390 <gbrowseImage> name=NC_007779:2590263..2591390 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2681394..2682521 <gbrowseImage> name=NC_010473:2681394..2682521 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
dapE6						CGSC:11587
dapE9						CGSC:11560
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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
JW2456	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCGTGCCCGGTTATTGAGCT Primer 2:CCGGCGACGAGCTGTTCCATGAT
7A8	Kohara Phage	Genobase	PMID:3038334
4C11	Kohara Phage	Genobase	PMID:3038334
nupC510::Tn10	Linked marker	CAG18468 = CGSC7410^[5]	est. P1 cotransduction: % ^[6]
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 88% ^[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:EG10208	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10208	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000202	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948313	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0204	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008142	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	DapE
Synonyms	N-succinyl-diaminopimelate deacylase^[1], MsgB^[2]^[1], B2472^[2]^[1], DapE^[2]^[1] , ECK2467, JW2456, msgB, b2472
Product description	N-succinyl-L-diaminopimelate desuccinylase subunit^[2]^[3]; Component of [[:Category:Complex:N-succinyl-L-diaminopimelate desuccinylase\|N-succinyl-L-diaminopimelate desuccinylase]]^[3] N-succinyl-diaminopimelate desuccinylase, DAP/lysine biosynthesis, contains Zn(2+)/Co(2+)^[4]
EC number (for enzymes)	3.5.1.18^[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				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0009014	succinyl-diaminopimelate desuccinylase activity	PMID:1644752	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001261	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002933	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008237	metallopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001261	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008237	metallopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002933	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01690	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	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:0009014	succinyl-diaminopimelate desuccinylase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01690	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009014	succinyl-diaminopimelate desuccinylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005941	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009014	succinyl-diaminopimelate desuccinylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.5.1.18	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_01690	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:IPR005941	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019877	diaminopimelate biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01690	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
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046983	protein dimerization activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011650	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050897	cobalt ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01690	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050897	cobalt ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0170	F	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 [[:Category:Complex:N-succinyl-L-diaminopimelate desuccinylase\|N-succinyl-L-diaminopimelate desuccinylase]]	could be indirect
Protein	groL		PMID:16606699	Experiment(s):EBI-1142975
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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 MSCPVIELTQ QLIRRPSLSP DDAGCQALLI ERLQAIGFTV ERMDFADTQN FWAWRGQGET LAFAGHTDVV PPGDADRWIN PPFEPTIRDG MLFGRGAADM KGSLAAMVVA AERFVAQHPN HTGRLAFLIT SDEEASAHNG TVKVVEALMA RNERLDYCLV GEPSSIEVVG DVVKNGRRGS LTCNLTIHGV QGHVAYPHLA DNPVHRAAPF LNELVAIEWD QGNEFFPATS MQIANIQAGT GSNNVIPGEL FVQFNFRFST ELTDEMIKAQ VLALLEKHQL RYTVDWWLSG QPFLTARGKL VDAVVNAVEH YNEIKPQLLT TGGTSDGRFI ARMGAQVVEL GPVNATIHKI NECVNAADLQ LLARMYQRIM EQLVA
Length	375
Mol. Wt	41.268 kDa
pI	5.3 (calculated)
Extinction coefficient	40,450 - 41,075 (calc based on 5 Y, 6 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	References
Domain	62..372	PF01546 Peptidase family M20/M25/M40	PMID:19920124
Domain	175..283	PF07687 Peptidase dimerisation 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=dapE 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:16130397	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948313	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008142	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AED7	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10208	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10208	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948313	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000202	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0204	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	2.84E+02	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	1286	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	263	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	997	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)
yffB
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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_000913:2589609..2589649 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:b2472 (EcoliWiki Page)	NCBI GEO profiles for dapE
microarray	GenExpDB:b2472 (EcoliWiki Page)	Summary of data for dapE 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 dapE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10208	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0204	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2472
EcoGene	EcoGene:EG10208	Escherichia coli str. K-12 substr. MG1655
[url ENTREZ] (EcoliWiki Page)	ENTREZ:X57403
RegulonDB	RegulonDB:ECK120000202	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008142	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
Arabidopsis thaliana	AT4G38220 (score: 1.000; bootstrap: 100%) AT1G44820 (score: 0.545) AT1G44180 (score: 0.527)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000031070 (score: 1.000; bootstrap: 100%) ENSBTAP00000028564 (score: 0.140)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000014619 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0037818 (score: 1.000; bootstrap: 100%) FBgn0039049 (score: 0.641) FBgn0039051 (score: 0.586) FBgn0039052 (score: 0.577) FBgn0039053 (score: 0.568) FBgn0039050 (score: 0.567)	From Inparanoid:20070104
Drosophila pseudoobscura	GA19815-PA (score: 1.000; bootstrap: 100%) GA19818-PA (score: 0.746)	From Inparanoid:20070104
Homo sapiens	ENSP00000232907 (score: 1.000; bootstrap: 51%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000004864 (score: 1.000; bootstrap: 56%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000015488 (score: 1.000; bootstrap: 100%) ENSMODP00000015494 (score: 0.519)	From Inparanoid:20070104
Mus musculus	MGI:87913 (score: 1.000; bootstrap: 56%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000015852 (score: 1.000; bootstrap: 48%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00023604001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	DAPE	From SHIGELLACYC
E. coli O157	DAPE	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)	PF01546 Peptidase family M20/M25/M40
Panther (EcoliWiki Page)	PTHR11014:SF5
Superfamily (EcoliWiki Page)	SUPERFAMILY:53187
Superfamily (EcoliWiki Page)	SUPERFAMILY:55031
Pfam (EcoliWiki Page)	PF07687 Peptidase dimerisation domain
PFAM (EcoliWiki Page)	PFAM:PF01546
EcoCyc	EcoCyc:EG10208	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10208	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000202	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0204	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008142	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 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).

dapE: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 dapE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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