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Escherichia coli K-12 substr. MG1655 Enzyme: N-succinyl-L-diaminopimelate desuccinylase




Gene: dapE Accession Numbers: EG10208 (EcoCyc), b2472, ECK2467

Synonyms: msgB

Regulation Summary Diagram

Regulation summary diagram for dapE

Subunit composition of N-succinyl-L-diaminopimelate desuccinylase = [DapE]4
         N-succinyl-L-diaminopimelate desuccinylase subunit = DapE

Summary:
The E. coli N-succinyl-L-diaminopimelate desuccinylase exists as a mixture of homodimers and homotetramers. It is a metalloenzyme, and requires either Co(II) or Zn(II) for activity. The enzyme is highly specific for its natural substrate [Lin88]. The dapE gene sequence bears similarity to argE, acetylornithine deacetylase [Bouvier92].

Locations: cytosol

Map Position: [2,589,629 -> 2,590,756] (55.81 centisomes, 201°)
Length: 1128 bp / 375 aa

Molecular Weight of Polypeptide: 41.269 kD (from nucleotide sequence), 40 kD (experimental) [Lin88]

Molecular Weight of Multimer: 160 kD (experimental) [Lin88]

Unification Links: ASAP:ABE-0008142, CGSC:876, EchoBASE:EB0204, EcoGene:EG10208, EcoliWiki:b2472, Entrez-Nucleotide:X57403, ModBase:P0AED7, OU-Microarray:b2472, PortEco:dapE, PR:PRO_000022403, Pride:P0AED7, Protein Model Portal:P0AED7, RefSeq:NP_416967, RegulonDB:EG10208, SMR:P0AED7, String:511145.b2472, Swiss-Model:P0AED7, UniProt:P0AED7

Relationship Links: InterPro:IN-FAMILY:IPR001261, InterPro:IN-FAMILY:IPR002933, InterPro:IN-FAMILY:IPR005941, InterPro:IN-FAMILY:IPR011650, Pfam:IN-FAMILY:PF01546, Pfam:IN-FAMILY:PF07687, Prosite:IN-FAMILY:PS00758, Prosite:IN-FAMILY:PS00759

In Paralogous Gene Group: 464 (3 members)

Gene-Reaction Schematic

Gene-Reaction Schematic


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006508 - proteolysis [GOA01a]
Inferred by computational analysisGO:0008152 - metabolic process [GOA01a]
Inferred by computational analysisGO:0008652 - cellular amino acid biosynthetic process [UniProtGOA11a]
Inferred by computational analysisGO:0009085 - lysine biosynthetic process [UniProtGOA11a]
Inferred by computational analysisGO:0009089 - lysine biosynthetic process via diaminopimelate [UniProtGOA12, GOA01a]
Inferred by computational analysisGO:0019877 - diaminopimelate biosynthetic process [UniProtGOA11a, GOA06]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0009014 - succinyl-diaminopimelate desuccinylase activity [GOA06, GOA01, GOA01a, Bouvier92]
Inferred by computational analysisGO:0008237 - metallopeptidase activity [GOA01a]
Inferred by computational analysisGO:0008270 - zinc ion binding [GOA06]
Inferred by computational analysisGO:0016787 - hydrolase activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0050897 - cobalt ion binding [GOA06]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08]

MultiFun Terms: metabolismbiosynthesis of building blocksamino acidslysine

Essentiality data for dapE knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB LennoxNo 37 Aerobic 7   No [Baba06, Comment 1]

Enzymatic reaction of: N-succinyl-L-diaminopimelate desuccinylase

Inferred from experiment

Synonyms: SDAP deacylase, succinyl-diaminopimelate-desuccinylase, succinyl DAP deacylase, N-succinyl-diaminopimelate deacylase

EC Number: 3.5.1.18

N-succinyl-L,L-2,6-diaminopimelate + H2O ⇄ L,L-diaminopimelate + succinate

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

In Pathways: aspartate superpathway, superpathway of L-lysine, L-threonine and L-methionine biosynthesis I, L-lysine biosynthesis I

Cofactors or Prosthetic Groups [ Comment 2]: Zn2+ [Lin88], Co2+ [Lin88]

Kinetic Parameters:
Substrate Km (μM) Citations
N-succinyl-L,L-2,6-diaminopimelate 400.0 [Lin88]

Sequence Features

Protein sequence of N-succinyl-L-diaminopimelate desuccinylase subunit with features indicated

Feature Class Location Citations Comment
Pfam PF01546 62 -> 371
Inferred by computational analysis[Finn14]
Peptidase_M20 : Peptidase family M20/M25/M40
Metal-Binding-Site 66
Inferred by computational analysis[UniProt15]
UniProt: Cobalt or zinc 1.
Active-Site 68
Inferred by computational analysis[UniProt15]
 
Metal-Binding-Site 99
Inferred by computational analysis[UniProt15]
UniProt: Cobalt or zinc 1.
Active-Site 133
Inferred by computational analysis[UniProt15]
UniProt: Proton acceptor.
Metal-Binding-Site 134
Inferred by computational analysis[UniProt15]
UniProt: Cobalt or zinc 2.
Metal-Binding-Site 162
Inferred by computational analysis[UniProt15]
UniProt: Cobalt or zinc 1.
Pfam PF07687 175 -> 282
Inferred by computational analysis[Finn14]
M20_dimer : Peptidase dimerisation domain
Metal-Binding-Site 348
Inferred by computational analysis[UniProt15]
UniProt: Cobalt or zinc 2.


Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b2472 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10208; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bouvier92: Bouvier J, Richaud C, Higgins W, Bogler O, Stragier P (1992). "Cloning, characterization, and expression of the dapE gene of Escherichia coli." J Bacteriol 1992;174(16);5265-71. PMID: 1644752

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Kindler60: Kindler SH, Gilvarg C "N-succinyl-L-alpha, epsilon-diaminopimelic acid deacylase." JBC 1960;235:3532-3535.

Lin88: Lin YK, Myhrman R, Schrag ML, Gelb MH (1988). "Bacterial N-succinyl-L-diaminopimelic acid desuccinylase. Purification, partial characterization, and substrate specificity." J Biol Chem 263(4);1622-7. PMID: 3276674

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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