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
3.5.1.18
-
RECOMMENDED NAME
GeneOntology No.
succinyl-diaminopimelate desuccinylase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
N-succinyl-LL-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
structure-activity relationship and catalytic mechanism of peptide bond cleavage by DapE enzymes, overview. The catalytic domain is composed of residues 1-179 and 293-376
-, P44514
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
hydrolysis of peptide bond
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
Lysine biosynthesis
-
lysine biosynthesis I
-
Metabolic pathways
-
Microbial metabolism in diverse environments
-
SYSTEMATIC NAME
IUBMB Comments
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Cgl1109
Corynebacterium glutamicum 534
Q59284
-
-
dapE-encoded N-succinyl-LL-diaminopimelic acid desuccinylase
-
-
N-succinyl-L,L-diaminopimelic acid desuccinylase
-
-
N-succinyl-L,L-diaminopimelic acid desuccinylase
P44514
-
N-succinyl-L,L-diaminopimelic acid desuccinylase
-
-
N-succinyl-L-alpha,epsilon-diaminopimelic acid deacylase
-
-
-
-
SDAP
-
-
-
-
sDap desuccinylase
-
-
-
-
succinyl-diaminopimelate desuccinylase
Q59284
-
succinyl-diaminopimelate desuccinylase
Corynebacterium glutamicum 534
Q59284
-
-
succinyl-diaminopimelate desuccinylase
-
-
succinyldiaminopimelate desuccinylase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9024-94-6
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
No.48292
-
-
Manually annotated by BRENDA team
Bacillus cereus No.48292
No.48292
-
-
Manually annotated by BRENDA team
Corynebacterium diphtheriae P.W.8
P.W.8
-
-
Manually annotated by BRENDA team
Corynebacterium glutamicum 534
-
Q59284
UniProt
Manually annotated by BRENDA team
M-26-26; wild type ATCC 9637
-
-
Manually annotated by BRENDA team
Escherichia coli M-26-26
M-26-26
-
-
Manually annotated by BRENDA team
Haemophilus influenzae RD
RD
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
-
DapE is involved in the meso-diaminopimelate (mDAP)/lysine biosynthetic pathway
metabolism
-, P44514
DapE is involved in the meso-diaminopimelate, mDAP/lysine biosynthetic pathway
physiological function
-
DapE is a critical bacterial enzyme for the construction of the bacterial cell wall.
physiological function
-, P44514
DapE is essential for cell growth and proliferation
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.26
-
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30C, ZnCo-loaded enzyme
0.73
-
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30C, Zn-loaded enzyme; pH 7.5, 30C, ZnZn-loaded enzyme
0.74
-
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30C, CoZn-loaded enzyme
0.99
-
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30C, CoCo-loaded enzyme; pH 7.5, 30C, Co-loaded enzyme
730
-
N-succinyl LL-diaminopimelic acid
-, P44514
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+
1.3
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
37C, pH 8.1
1.3
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
in the presence of Zn2+
1.5
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
37C, pH 8.1, in the presence of Co2+
1.6
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
in the presence of Co2+
4.7
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
in the presence of Co2+
0.73
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, wild-type enzyme
-
1.4
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, mutant H67A
-
0.65
-
N-succinyl-LL-diaminopimelate
-
mutant enzyme E134D at pH 7.5
0.73
-
N-succinyl-LL-diaminopimelate
-
wild type enzyme at pH 7.5
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
140
-
N-succinyl LL-diaminopimelic acid
-, P44514
pH not specified in the publication, temperature not specified in the publication
0.0555
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
in the presence of zinc
1.5
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, mutant H67A
-
140
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, wild-type enzyme
-
0.13
-
N-succinyl-LL-diaminopimelate
-
mutant enzyme E134D at pH 7.5
140
-
N-succinyl-LL-diaminopimelate
-
wild type enzyme at pH 7.5
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1.1
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, mutant H67A
0
204
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, wild-type enzyme
0
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.17
-
-
mutant enzyme E134D at pH 7.5
180
-
-
wild type enzyme at pH 7.5
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
-
-
assay at
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6
9
-
pH 6: 60%, pH 9: 65% of maximal activity
6
9
-
activity below pH 6.0 was not observed
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
-
assay at
PDB
SCOP
CATH
ORGANISM
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
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
41500
-
-
SDS-PAGE
83000
-
-, P44514
about
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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
-, Q59284
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
-, P44514
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6
9
-
activity below pH 6.0 was not observed
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
fast-flow Q-sepharose anionexchange column chromatography
-
recombinant wild-type enzyme and mutants from Escherichia coli BL21
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
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+
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
drug development
-, P44514
development of antimicrobial agents that target DapE
drug development
-
protein may be potential target for developing a vaccine against Leishmania infantum