Information on EC 3.5.1.18 - succinyl-diaminopimelate desuccinylase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
3.5.1.18
-
RECOMMENDED NAME
GeneOntology No.
succinyl-diaminopimelate desuccinylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
N-succinyl-LL-2,6-diaminoheptanedioate + H2O = succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of peptide bond
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
L-lysine biosynthesis I
-
-
Lysine biosynthesis
-
-
lysine metabolism
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
SYSTEMATIC NAME
IUBMB Comments
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase
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CAS REGISTRY NUMBER
COMMENTARY hide
9024-94-6
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
No.48292
-
-
Manually annotated by BRENDA team
Bacillus cereus No.48292
No.48292
-
-
Manually annotated by BRENDA team
P.W.8
-
-
Manually annotated by BRENDA team
M-26-26
-
-
Manually annotated by BRENDA team
RD
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
gene dapE or Rv1202
SwissProt
Manually annotated by BRENDA team
gene dapE
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
?
show the reaction diagram
-
high stereospecificity
-
?
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
N-succinyl-DL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
N-succinyl-LL-2,6-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
N-succinyl-LL-diaminopimelate + H2O
?
show the reaction diagram
-
-
-
-
?
N-succinyl-LL-diaminopimelic acid + H2O
?
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Al3+
-
required
Cd2+
-
65% of activity with Zn2+
Fe3+
-
required
Mg2+
-
required
Ni2+
-
required
sulfate
in one of the monomers of the ZnZn_DapE structure, both of these residues form a charged dipole interaction with a sulfate ion, a possible mimic of the carboxylic group of the substrate
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2-carboxyethyl)-phosphonic acid
-
slight inhibition
2-amino-6-[(2-methylpropanoyl)amino]heptanedioic acid
-
slight inhibition
2-thiopheneboronic acid
-
noncompetitive
3-mercaptobenzoic acid
-
-
4-sulfanylbutanoic acid
-
-
aceto-hydroxamic acid
-
slight inhibition
D,L-diaminopimelic acid
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competitive
D-captopril
-
-
-
D-penicillamine
-
competitive
EDTA
-
complete
enalapril
-
maleate salt, slight inhibition
L,L-diaminopimelic acid
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competitive
L-captopril
L-Penicillamine
-
-
N-(benzyloxycarbonyl)hydroxylamine
-
slight inhibition
N-phenyl-thiourea
-
slight inhibition
phenylboronic acid
-
competitive
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.26 - 0.99
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
730
N-succinyl LL-diaminopimelic acid
pH not specified in the publication, temperature not specified in the publication
3.2
N-succinyl-DL-2,6-diaminoheptanedioate
-
in the presence of Zn2+
0.8 - 4.7
N-succinyl-LL-2,6-diaminoheptanedioate
0.73 - 1.4
N-succinyl-LL-2,6-diaminopimelic acid
0.65 - 0.73
N-succinyl-LL-diaminopimelate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
140
N-succinyl LL-diaminopimelic acid
Haemophilus influenzae
P44514
pH not specified in the publication, temperature not specified in the publication
0.0555 - 114
N-succinyl-LL-2,6-diaminoheptanedioate
1.5 - 140
N-succinyl-LL-2,6-diaminopimelic acid
0.13 - 140
N-succinyl-LL-diaminopimelate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.1 - 204
N-succinyl-LL-2,6-diaminopimelic acid
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.8
(2-carboxyethyl)-phosphonic acid
-
pH not specified in the publication, temperature not specified in the publication
0.067
2-thiopheneboronic acid
-
pH not specified in the publication, temperature not specified in the publication
0.0018
L-captopril
0.0046
L-Penicillamine
-
pH not specified in the publication, temperature not specified in the publication
0.0569
phenylboronic acid
-
pH not specified in the publication, temperature not specified in the publication
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.62
(2-carboxyethyl)-phosphonic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
17
2-amino-6-[(2-methylpropanoyl)amino]heptanedioic acid
Haemophilus influenzae
-
pH 7.5, 25C
0.092
2-thiopheneboronic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
0.034
3-mercaptobenzoic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
0.043
4-sulfanylbutanoic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
1
aceto-hydroxamic acid
Haemophilus influenzae
-
above, pH not specified in the publication, temperature not specified in the publication
0.042
D-captopril
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
-
0.05
D-penicillamine
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
1
enalapril
Haemophilus influenzae
-
above, pH not specified in the publication, temperature not specified in the publication
0.0033
L-captopril
0.0137
L-Penicillamine
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
1
N-(benzyloxycarbonyl)hydroxylamine
Haemophilus influenzae
-
above, pH not specified in the publication, temperature not specified in the publication
0.01
N-phenyl-thiourea
Haemophilus influenzae
-
above, pH not specified in the publication, temperature not specified in the publication
0.107
phenylboronic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.17
-
mutant enzyme E134D at pH 7.5
180
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wild type enzyme at pH 7.5
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23200
catalytic domain, dynamic light scattering
28400
-
catalytic domain, gel filtration
41500
-
SDS-PAGE
82600
-
wild-type enzyme, gel filtration
83200
-
wild-type enzyme, dynamic light scattering
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
-
2 * 41600, estimated from amino acid sequence; 2 * 42000, SD-PAGE
monomer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting nanodroplet vapor diffusion method, using 6 mM ZnCl2, 43.1% (w/v) polyethylene glycol 400, 0.2 M sodium chloride, 0.1 M sodium/potassium phosphate pH 6.4, at 20C
crystal structure, PDB ID 3IC1, analysis, comparison with the structure of N-acetyl-L-ornithine deacetylase, EC 3.5.1.16, overview
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purified recombinant wild-type and mutant G172D enzymes, apoform and Zn2+-bound enzyme, using 400 nl of a precipitant solution containing 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG 3350, and 400 nl of 15 mg/ml of protein in crystallization buffer, with or without 1 mM ZnCl2, within 14 days, X-ray diffraction structure determination and analysis at 1.84 A resolution
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ultrapure recombinant DapE with one and two zinc ions bound in the active site, respectively, at 16C, by vapor diffusion in hanging drops containing 1 ml of precipitant solution containing 1 M ammonium sulfate, 0.2 M NaCl, and 0.1 M Na acetate, pH 4.4, and 0.001 ml of 13 mg/ml of DapE with three equivalents of zinc, 2 weeks, X-ray diffraction structure determination and analysis at 2.0-2.3 A resolution
purified recombinant His-tagged enzyme, hanging drop vapour diffusion method, 0.001-0.002 ml of 3-7 mg/ml protein in 50 mM Bis-Tris, pH 6.0, 200 mM NaCl, 0.5 mM TCEP is mixed with 0.001-0.002 ml reservoir solution, containing 5-10% w/v PEG 4000 or PEG 3350, 35-120 mM ammonium sulfate, 100 mM sodium acetate, pH 4.1-4.6, and equilibrated against 0.9 ml reservoir solution, at room temperature, 1 day, method optimization, X-ray diffraction structure determination and analysis at 2.4-2.58 A resolution, two crystal forms
purified recombinant enzyme, apoform and Zn2+-bound enzyme, using 400 nl of a precipitant solution containing 20% v/v 1,4-butanediol, 0.1 M sodium acetate, pH 4.5, and 400 nl of 19 mg/ml protein in crystallization buffer, with or without 1 mM ZnCl2, within 14 days, X-ray diffraction structure determination and analysis at 1.65 A resolution
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9
-
activity below pH 6.0 was not observed
669532
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
fast-flow Q-sepharose anionexchange column chromatography
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recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3)/pMAGIC by nickel affinity chromatography and gel filtration
recombinant N-terminally His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3)/pMAGIC by nickel affinity chromatography and gel filtration
-
recombinant wild-type enzyme and mutants from Escherichia coli BL21
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
-
expressed in Escherichia coli XL1-Blue cells and in Salmonella enterica strain TN5911
-
expression in Escherichia coli
-
gene dapE, expression of wild-type enzyme and mutants in Escherichia coli BL21, subcloning in Escherichia coli JM109
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gene dape, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) chaperone combination 3 (cc3) cells, which co-express the chaperones GroEL and GroES in order to increase the yield of soluble protein expression
gene dapE, recombinant expression of N-terminally His6-tagged enzyme, containing a TEV protease recognition site followed by the DapE catalytic domain, in an Escherichia coli strain BL21(DE3) derivative that harbors the pMAGIC plasmid encoding one rare Escherichia coli Arg tRNA (covering codons AGG/AGA)
gene dapE, recombinant expression of N-terminally His6-tagged wild-type and mutant enzymes, containing a TEV protease recognition site followed by the DapE catalytic domain, in an Escherichia coli strain BL21(DE3) derivative that harbors the pMAGIC plasmid encoding one rare Escherichia coli Arg tRNA (covering codons AGG/AGA)
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gene dapE, sequence comparison
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E134A
-
Glu134 replaced by alanine
E134D
-
Glu134 replaced by aspartate
H349A
-
site-directed mutagenesis, inactive mutant
H67A
-
site-directed mutagenesis, the mutant shows 180fold decreased activity compred to the wild-type enzyme. Approximately 70% of the maximal catalytic activity is recovered after the addition of 1 equiv of Zn2+
T325A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
T325C
-
site-directed mutagenesis, inactive mutant
T325S
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
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