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Information on EC 2.3.1.117 - 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
for references in articles please use BRENDA:EC2.3.1.117
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EC Tree 2 Transferases
2.3 Acyltransferases
2.3.1 Transferring groups other than aminoacyl groups
2.3.1.117 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
IUBMB Comments
Involved in the biosynthesis of lysine in bacteria (including cyanobacteria) and higher plants. The 1992 edition of the Enzyme List erroneously gave the name 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase to this enzyme.
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
- 2.3.1.117
- l-lysine
- meso-diaminopimelate
- diaminopimelate
- trimer
- glutamicum
-
left-handed
- peptidoglycan
- corynebacterium
-
beta-helix
- tuberculosis
-
desuccinylase
-
succinylated
- hexapeptide
- dihydrodipicolinate
-
lbetah
Reaction Schemes
showSynonyms
tetrahydrodipicolinate n-succinyltransferase, tetrahydrodipicolinate succinylase, mtb-dapd, tetrahydrodipicolinate-n-succinyltransferase, succinyl-coa:tetrahydrodipicolinate n-succinyltransferase, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
DapD
succinyl-CoA:tetrahydrodipicolinate N-succinyltransferase
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-
-
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succinyltransferase, tetrahydrodipicolinate
-
-
-
-
tetrahydrodipicolinate N-succinyltransferase
tetrahydrodipicolinate succinylase
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-
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tetrahydrodipicolinate succinyltransferase
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-
-
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tetrahydrodipicolinate-N-succinyltransferase
tetrahydrodipicolinate N-succinyltransferase
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-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O = CoA + N-succinyl-L-2-amino-6-oxoheptanedioate
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Acyl group transfer
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-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
MetaCyc
L-lysine biosynthesis I
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SYSTEMATIC NAME
IUBMB Comments
succinyl-CoA:(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Involved in the biosynthesis of lysine in bacteria (including cyanobacteria) and higher plants. The 1992 edition of the Enzyme List erroneously gave the name 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase to this enzyme.
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CAS REGISTRY NUMBER
COMMENTARY
88086-34-4
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O
CoA + N-succinyl-L-2-amino-6-oxoheptanedioate
succinyl-CoA + 3,4-dihydro-2H-1,4-thiazine-3,5-dicarboxylic acid
?
-
Substrates: -
Products: -
Products: -
?
succinyl-CoA + 6-amino-2-hydroxypimelic acid
CoA + N-succinyl-6-amino-2-hydroxypimelate
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Substrates: -
Products: -
Products: -
?
succinyl-CoA + L-6-amino-L-2-hydroxypimelic acid
CoA + N-succinyl-L-6-amino-L-2-hydroxypimelate
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Substrates: mixture of isomers
Products: -
Products: -
?
succinyl-CoA + tetrahydrodipicolinate
CoA + (2S)-2-(3-carboxypropanamido)-6-oxoheptanedioate
Substrates: -
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: -
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: involved in the four-step succinylase branch of the L-lysine biosynthetic pathway
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: -
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
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Substrates: product formation is strongly preferred
Products: -
Products: -
r
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: involved in the biosynthesis of lysine in bacteria, blue-green algae and higher plants
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: involved in the biosynthesis of lysine in bacteria, blue-green algae and higher plants
Products: -
Products: -
r
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: -
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: involved in the biosynthesis of lysine in bacteria, blue-green algae and higher plants
Products: -
Products: -
?
succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O
CoA + N-succinyl-L-2-amino-6-oxoheptanedioate
-
Substrates: the enzyme is absolutely specific for the L-2-aminopimelate enantiomer
Products: -
Products: -
?
succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O
CoA + N-succinyl-L-2-amino-6-oxoheptanedioate
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Substrates: the enzyme is absolutely specific for the L-2-aminopimelate enantiomer, L-2-aminopimelate and weak inhibitor D-2-aminopimelate bind at the same site of the enzyme. Binding interaction analysis of the ligands in the enzyme active site suggests a misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition
Products: -
Products: -
?
succinyl-CoA + L-2-aminopimelate
CoA + N-succinyl-L-aminopimelate
Substrates: -
Products: -
Products: -
?
succinyl-CoA + L-2-aminopimelate
CoA + N-succinyl-L-aminopimelate
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Substrates: tetrahydrodipicolinate analogue
Products: -
Products: -
?
succinyl-CoA + tetrahydrodipicolinate
?
-
Substrates: -
Products: -
Products: -
?
additional information
?
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Substrates: no activity ith L-lysine, adipic acid, alpha-amino-adipic acid, L-epsilon-acetyl-lysine, L-glutamate, L-glutamine, L-norleucine, substrate specificity for DapD, overview. Binding of CoA to PaDapD does not induce any large conformational changes, ternary complex structure of DapD with bound CoA and succinate, overview
Products: -
Products: -
?
additional information
?
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Substrates: no substrates: 5,5'-dithio-bis-(2-nitrobenzoic acid), L-aminoadipic acid, poor substrate: acetyl-CoA
Products: -
Products: -
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O
CoA + N-succinyl-L-2-amino-6-oxoheptanedioate
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Substrates: the enzyme is absolutely specific for the L-2-aminopimelate enantiomer
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: involved in the four-step succinylase branch of the L-lysine biosynthetic pathway
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: -
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: involved in the biosynthesis of lysine in bacteria, blue-green algae and higher plants
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: involved in the biosynthesis of lysine in bacteria, blue-green algae and higher plants
Products: -
Products: -
r
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: -
Products: -
Products: -
?
succinyl-CoA + (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CoA + (2S)-2-[(3-carboxypropanoyl)amino]-6-oxoheptanedioic acid
-
Substrates: involved in the biosynthesis of lysine in bacteria, blue-green algae and higher plants
Products: -
Products: -
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
stabilizes quartenary enzyme structure, slight increase of enzyme activity
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
acetate
caused by inhibition of succinyl-CoA-binding or pH effect
D-2-aminopimelate
-
competitive vs. L-2-aminopimelate and tetrahydropicolinate
D-2-aminopimelate
-
very weak competitive inhibition, L-2-aminopimelate and D-2-aminopimelate bind at the same site of the enzyme. Binding interaction analysis of the ligands in the enzyme active site suggests a misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Tuberculosis
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of tetrahydrodipicolinate-N-succinyltransferase (Rv1201c) from Mycobacterium tuberculosis.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
reaction kinetics for DapD, overview
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
enzyme is a member of the hexapeptide acyltransferase superfamily
-
-
brenda
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
-
the DAP biosynthesis pathway is present in most Gram-negative bacteria and mycobacteria
metabolism
-
tetrahydrodipicolinate N-succinyltransferase catalyses the transfer of the succinyl moiety of succinyl-CoA to the alpha-amino group of tetrahydrodipicolinate, the first committed step in the succinylase branch of the DAP biosynthesis pathway, diaminopimelic acid pathway of lysine biosynthesis, overview
physiological function
part of L-lysine biosynthetic pathway
Show AA Sequence and Transmembrane Helices (21566 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
trimer
trimer
-
the subunit of PaDapD consists of three domains, the N-terminal globular domain, a central domain, and a C-terminal domain, overview
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
structure in complex with succinyl-CoA. Enzyme functions as a trimer, and each monomer consists of an N-terminal helical domain, a left-handed beta-helix domain, and a beta C-terminal domain. The position of the C-terminal domain changes slightly as the cofactor binds to the enzyme. The structure of DapD in complex with the substrate analogue 2-aminopimelate reveals that the analogue is stabilized by conserved residues
crystal structure of DapD from Escherichia coli at 2.0 A resolution is shown. Comparison of the structure with the homologous enzyme from Mycobacterium bovis reveals the C-terminal helix undergoes a large rearrangement upon substrate binding, which contributes to cooperativity in substrate binding
crystallized in the cubic space group I23 or I213. Diffraction data analysis indicates the presence of five molecules per asymmetric unit. Data exhibit icosahedral point-group symmetry. Enzyme might assembles into a 60-mer exhibiting 235 point-group symmetry and crystallizes as such in space group I23. In this case, the combination of crystallographic and noncrystallographic symmetry elements results in an arrangement of the icosahedrons in the cubic crystal with one pentamer in the asymmetric unit. Another explanation is that the packing of the molecules itself mimics icosahedral symmetry. In this case both space groups I23 and I213 would be possible
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crystal structure in complex with L-2-aminopimelate/coenzyme A and L-2-amino-6-oxopimelate/coenzyme A at 2.0 A resolution, hanging drop vapor diffusion from solutions of 10-13% poly(ethylene glycol) 4000, 94 mM MES, pH 6.4, 94 mM ammonium sulfate, and 4.7% 2-propanol in the presence of 16 mM (D,L)-2-aminopimelate and 2.5 mM CoA
-
crystal structure of the enzyme in ternary complexes with pimelate/succinyl-CoA and L-2-aminopimelate with the nonreactive cofactor analog succinamide-CoA, 2.3 and 2.0 A resolution, crystals are prepared by cocrystallization using the hanging drop vapor diffusion method, drops are formed by mixing 0.005 ml 27 mg/ml enzyme with an equal volume of 17% poly(ethylene glycol) 4000, 188 mM ammonium sulfate, 94 mM MES, pH 6.4, 4.7% 2-propanol, 20 mM pimelate, and 5 mM succinyl-CoA or 5 mM succinamide-CoA
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crystallized from solutions of 16% poly(ethylene glycol) 4000, 200 mM ammonium sulfate, 100 mM HEPES, pH 7.5, and 10% 2-propanol, crystals belong to space group P21, X-ray structure refined to 2.2 A resolution
-
purified recombinant His6-tagged DapD with bound L-2-aminopimelate and D-2-aminopimelate or in complex with CoA/succinate, hanging drop vapour diffusion method, mixing of 0.002 ml of 26 mg/ml protein in 25 mM Tris-HCl pH 8.0, and 150 mM NaCl, with or without 10-15 mM CoA, with 0.002 ml of reservoir solution containing 19-20% of PEG3350, 0.3-0.4 M succinate, pH 6.2, and equilibration against reservoir solution for 1-2 days, incubation of the enzyme with formyl-CoA leads to better crystals, soaking of apoenzyme crystals in solution containing L-2-aminopimelate and D-2-aminopimelate, the CoA-complex also contains a succinatemolecule bound next to the acceptor arm of the CoA in the active site cleft, X-ray diffraction structure determination and analysis at 1.8-2.95 A resolution, molecular replacement
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
binary complex of Mtb-DapD and succinyl-CoA
additional information
-
binary complex of Mtb-DapD and succinyl-CoA
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
MnCl2, ammonium sulfate, DEAE-cellulose, acid treatment, hydroxyapatite, phenyl-Sepharose, chromatofocusing
-
recombinant His-tagged DapD from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, removal of te the N-terminal His6-tag by thrombin cleavage is not successful
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene dapD, phylogenetic tree, expression of His-tagged DapD in Escherichia coli strain BL21(DE3)
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
DapA is not an optimal target for drug development against Pseudomonas aeruginosa
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Born, T.L.; Blanchard, J.S.
Structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis
Curr. Opin. Chem. Biol.
3
607-613
1999
Escherichia coli, Mycobacterium tuberculosis variant bovis
brenda
Simms, S.A.; Voige, W.H.; Gilvarg, C.
Purification and characterization of succinyl-CoA: tetrahydrodipicolinate N-succinyltransferase from Escherichia coli
J. Biol. Chem.
259
2734-2741
1984
Escherichia coli
brenda
Berges, D.A.; DeWolf, W.E.; Dunn, G.L.; Newmann, D.J.; Schmidt, S.J.; Taggart, J.J.; Gilvarg, C.
Studies on the active site of succinyl-CoA:tetrahydrodipicolinate N-succinyltransferase. Characterization using analogs of tetrahydrodipicolinate
J. Biol. Chem.
261
6160-6167
1986
Escherichia coli
brenda
Beaman, T.W.; Binder, D.A.; Blanchard, J.S.; Roderick, S.L.
Three-dimensional structure of tetrahydrodipicolinate N-succinyltransferase
Biochemistry
36
489-494
1997
Mycobacterium tuberculosis variant bovis
brenda
Beaman, T.W.; Blanchard, J.S.; Roderick, S.L.
The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase
Biochemistry
37
10363-10369
1998
Mycobacterium tuberculosis variant bovis
brenda
Shaw-Reid, C.A.; McCormick, M.M.; Sinskey, A.J.; Stephanopoulos, G.
Flux through the tetrahydrodipicolinate succinylase pathway is dispensable for L-lysine production in Corynebacterium glutamicum
Appl. Microbiol. Biotechnol.
51
325-333
1999
Corynebacterium glutamicum
brenda
Beaman, T.W.; Vogel, K.W.; Drueckhammer, D.G.; Blanchard, J.S.; Roderick, S.L.
Acyl group specificity at the active site of tetrahydrodipicolinate N-succinyltransferase
Protein Sci.
11
974-979
2002
Mycobacterium tuberculosis variant bovis
brenda
Schuldt, L.; Weyand, S.; Kefala, G.; Weiss, M.S.
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of tetrahydrodipicolinate-N-succinyltransferase (Rv1201c) from Mycobacterium tuberculosis
Acta Crystallogr. Sect. F
64
863-866
2008
Mycobacterium tuberculosis
brenda
Nguyen, L.; Kozlov, G.; Gehring, K.
Structure of Escherichia coli tetrahydrodipicolinate N-succinyltransferase reveals the role of a conserved C-terminal helix in cooperative substrate binding
FEBS Lett.
582
623-626
2008
Escherichia coli (Q8X8Y7), Escherichia coli
brenda
Schuldt, L.; Weyand, S.; Kefala, G.; Weiss, M.S.
The three-dimensional Structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism
J. Mol. Biol.
389
863-879
2009
Mycobacterium tuberculosis (P9WP21), Mycobacterium tuberculosis
brenda
Schnell, R.; Oehlmann, W.; Sandalova, T.; Braun, Y.; Huck, C.; Maringer, M.; Singh, M.; Schneider, G.
Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion
PLoS ONE
7
e31133
2012
Pseudomonas aeruginosa
brenda
Sagong, H.Y.; Kim, K.J.
Crystal structure and biochemical characterization of tetrahydrodipicolinate N-succinyltransferase from Corynebacterium glutamicum
J. Agric. Food Chem.
63
10641-10646
2015
Corynebacterium glutamicum (Q8NRE3), Corynebacterium glutamicum, Corynebacterium glutamicum DSM 20300 (Q8NRE3)
brenda
Manning, M.E.; Danson, E.J.; Calderone, C.T.
Functional chararacterization of the enzymes TabB and TabD involved in tabtoxin biosynthesis by Pseudomonas syringae
Biochem. Biophys. Res. Commun.
496
212-217
2018
Pseudomonas amygdali pv. tabaci (P31852)
brenda
EXTERNAL LINKS (specific for EC-Number 2.3.1.117)
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