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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: ?

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)
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: ?

GO Terms:

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

MultiFun Terms: metabolism biosynthesis of building blocks amino acids lysine

Essentiality data for dapE knockouts: ?

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

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

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 reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

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

Feature Class Location Citations Comment
Metal-Binding-Site 66
[UniProt10a]
UniProt: Cobalt or zinc 1; Non-Experimental Qualifier: by similarity;
Active-Site 68
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 99
[UniProt10a]
UniProt: Cobalt or zinc 1; Non-Experimental Qualifier: by similarity;
Active-Site 133
[UniProt10a]
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 134
[UniProt10a]
UniProt: Cobalt or zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 162
[UniProt10a]
UniProt: Cobalt or zinc 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 348
[UniProt10a]
UniProt: Cobalt or zinc 2; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

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

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." 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."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, BIOCYC14A.