Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

MetaCyc Enzyme: tetrahydrodipicolinate succinylase

Gene: dapD Accession Numbers: EG10207 (MetaCyc), b0166, ECK0164

Synonyms: ssa

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of tetrahydrodipicolinate succinylase = [DapD]2
         tetrahydrodipicolinate succinylase = DapD

Summary:
Tetrahydrodipicolinate succinylase (DapD) catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate, and is a key enzyme in the E. coli lysine biosynthetic pathway [Simms84].

A crystal structure of DapD from E. coli O157:H7 has been solved [Nguyen08].

Expression of dapD is repressed by lysine [Richaud84, Ou08] via ArgP [Marbaniang11].

DapD: "diaminopimelate biosynthesis D" [Bukhari71]

Citations: [Degryse91, Maringanti99, Berges86]

Locations: cytosol

Map Position: [185,123 <- 185,947]

Molecular Weight of Polypeptide: 29.892 kD (from nucleotide sequence), 31 kD (experimental) [Simms84 ]

Molecular Weight of Multimer: 72 kD (experimental) [Simms84]

Unification Links: ASAP:ABE-0000565 , CGSC:877 , DIP:DIP-31866N , EchoBASE:EB0203 , EcoGene:EG10207 , EcoliWiki:b0166 , Entrez-Nucleotide:K02970 , ModBase:P0A9D8 , OU-Microarray:b0166 , PortEco:dapD , PR:PRO_000022402 , Pride:P0A9D8 , Protein Model Portal:P0A9D8 , RefSeq:NP_414708 , RegulonDB:EG10207 , SMR:P0A9D8 , String:511145.b0166 , Swiss-Model:P0A9D8 , UniProt:P0A9D8

Relationship Links: InterPro:IN-FAMILY:IPR001451 , InterPro:IN-FAMILY:IPR005664 , InterPro:IN-FAMILY:IPR011004 , InterPro:IN-FAMILY:IPR018357 , InterPro:IN-FAMILY:IPR023180 , Panther:IN-FAMILY:PTHR19136:SF52 , Pfam:IN-FAMILY:PF00132 , Prosite:IN-FAMILY:PS00101

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009085 - lysine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, Simms84]
GO:0019877 - diaminopimelate biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Bukhari71]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0009089 - lysine biosynthetic process via diaminopimelate Inferred by computational analysis [UniProtGOA12, GOA01]
Molecular Function: GO:0008666 - 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Simms84]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016746 - transferase activity, transferring acyl groups Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids lysine

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: tetrahydrodipicolinate succinylase

EC Number: 2.3.1.117

(S)-2,3,4,5-tetrahydrodipicolinate + succinyl-CoA + H2O <=> N-succinyl-2-amino-6-ketopimelate + coenzyme A

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

The reaction is physiologically favored in the direction shown. [Simms84]

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

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
The E. coli strain used for purification of the enzyme by [Simms84] was not specified.

The reaction equilibrium lies predominantly in favor of product formation in physiological pH: the reaction rate in the forward direction is 380-fold greater than in the reverse direction [Simms84].

Inhibitors (Unknown Mechanism): Zn2+ [Simms84] , Cu2+ [Simms84] , Co2+ [Simms84]

Kinetic Parameters:

Substrate
Km (μM)
Citations
succinyl-CoA
15.0
[Simms84, BRENDA14]
(S)-2,3,4,5-tetrahydrodipicolinate
20.0
[Berges86, BRENDA14]
(S)-2,3,4,5-tetrahydrodipicolinate
22.0
[Simms84, BRENDA14]

pH(opt) (forward direction): 8.2 [Simms84]

pH(opt): 8.2 [BRENDA14, Simms84]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 31
[Richaud84, UniProt10]
Alternate sequence: D; UniProt: (in Ref. 1; AAA23667);
Acetylation-Modification 85
[Yu08b]
 
Acetylation-Modification 100
[Yu08b]
 
Amino-Acid-Sites-That-Bind 104
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 141
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 163
[Richaud84, UniProt10]
Alternate sequence: R; UniProt: (in Ref. 1; AAA23667);
Sequence-Conflict 177
[Richaud84, UniProt10]
Alternate sequence: M; UniProt: (in Ref. 1; AAA23667);
Sequence-Conflict 190
[Richaud84, UniProt10]
Alternate sequence: L; UniProt: (in Ref. 1; AAA23667);

History:
10/20/97 Gene b0166 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10207; confirmed by SwissProt match.


References

Berges86: Berges DA, DeWolf WE, Dunn GL, Newman DJ, Schmidt SJ, Taggart JJ, Gilvarg C (1986). "Studies on the active site of succinyl-CoA:tetrahydrodipicolinate N-succinyltransferase. Characterization using analogs of tetrahydrodipicolinate." J Biol Chem 261(14);6160-7. PMID: 3700390

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Bukhari71: Bukhari AI, Taylor AL (1971). "Genetic analysis of diaminopimelic acid- and lysine-requiring mutants of Escherichia coli." J Bacteriol 105(3);844-54. PMID: 4926684

Degryse91: Degryse E (1991). "Polymorphism in the dgt-dapD-tsf region of Escherichia coli K-12 strains." Gene 102(1);141-2. PMID: 1677906

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

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Marbaniang11: Marbaniang CN, Gowrishankar J (2011). "Role of ArgP (IciA) in lysine-mediated repression in Escherichia coli." J Bacteriol 193(21);5985-96. PMID: 21890697

Maringanti99: Maringanti S, Imlay JA (1999). "An intracellular iron chelator pleiotropically suppresses enzymatic and growth defects of superoxide dismutase-deficient Escherichia coli." J Bacteriol 181(12);3792-802. PMID: 10368155

Nguyen08: Nguyen L, Kozlov G, Gehring K (2008). "Structure of Escherichia coli tetrahydrodipicolinate N-succinyltransferase reveals the role of a conserved C-terminal helix in cooperative substrate binding." FEBS Lett 582(5);623-6. PMID: 18242192

Ou08: Ou J, Yamada T, Nagahisa K, Hirasawa T, Furusawa C, Yomo T, Shimizu H (2008). "Dynamic change in promoter activation during lysine biosynthesis in Escherichia coli cells." Mol Biosyst 4(2);128-34. PMID: 18213406

Richaud84: Richaud C, Richaud F, Martin C, Haziza C, Patte JC (1984). "Regulation of expression and nucleotide sequence of the Escherichia coli dapD gene." J Biol Chem 1984;259(23);14824-8. PMID: 6094577

Simms84: Simms SA, Voige WH, Gilvarg C (1984). "Purification and characterization of succinyl-CoA: tetrahydrodipicolinate N-succinyltransferase from Escherichia coli." J Biol Chem 1984;259(5);2734-41. PMID: 6365916

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

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

Yu08b: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, biocyc14.