BRENDA - Enzyme Database
show all sequences of 4.1.1.20

Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor

Ray, S.S.; Bonanno, J.B.; Rajashankar, K.R.; Pinho, M.G.; He, G.; De Lencastre, H.; Tomasz, A.; Burley, S.K.; Structure 10, 1499-1508 (2002)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression in Escherichia coli
Methanocaldococcus jannaschii
Crystallization (Commentary)
Crystallization
Organism
co-crystals of DAPDC and azelaic acid and L-lysine at 2.6 A and 2.0 A resolution, respectively, hanging drop vapor-diffusion, 12% polyethylene glycol 6000, 100 mm Tris-Cl, pH 8.0, 20 mM MgCl2 and 10 mM L-lysine
Methanocaldococcus jannaschii
Inhibitors
Inhibitors
Commentary
Organism
Structure
1,5-Diaminopentane
-
Methanocaldococcus jannaschii
1,6-diaminohexane
-
Methanocaldococcus jannaschii
1,7-Diaminoheptane
-
Methanocaldococcus jannaschii
adipic acid
-
Methanocaldococcus jannaschii
azelaic acid
-
Methanocaldococcus jannaschii
caproic acid
-
Methanocaldococcus jannaschii
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
50000
-
x * 50000, mass spectrometry
Methanocaldococcus jannaschii
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
meso-2,6-Diaminoheptanedioate
Methanocaldococcus jannaschii
last step in L-lysine biosynthesis
L-Lysine + CO2
-
Methanocaldococcus jannaschii
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Methanocaldococcus jannaschii
-
-
-
Purification (Commentary)
Commentary
Organism
recombinant DAPDC
Methanocaldococcus jannaschii
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
meso-2,6-Diaminoheptanedioate
-
653897
Methanocaldococcus jannaschii
L-Lysine + CO2
-
653897
Methanocaldococcus jannaschii
?
meso-2,6-Diaminoheptanedioate
last step in L-lysine biosynthesis
653897
Methanocaldococcus jannaschii
L-Lysine + CO2
-
653897
Methanocaldococcus jannaschii
?
Subunits
Subunits
Commentary
Organism
?
x * 50000, mass spectrometry
Methanocaldococcus jannaschii
Ki Value [mM]
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
0.0024
-
1,6-diaminohexane
-
Methanocaldococcus jannaschii
0.0025
-
1,7-Diaminoheptane
-
Methanocaldococcus jannaschii
0.004
-
1,5-Diaminopentane
-
Methanocaldococcus jannaschii
0.089
-
azelaic acid
-
Methanocaldococcus jannaschii
0.13
-
adipic acid
-
Methanocaldococcus jannaschii
0.21
-
caproic acid
-
Methanocaldococcus jannaschii
Cloned(Commentary) (protein specific)
Commentary
Organism
expression in Escherichia coli
Methanocaldococcus jannaschii
Crystallization (Commentary) (protein specific)
Crystallization
Organism
co-crystals of DAPDC and azelaic acid and L-lysine at 2.6 A and 2.0 A resolution, respectively, hanging drop vapor-diffusion, 12% polyethylene glycol 6000, 100 mm Tris-Cl, pH 8.0, 20 mM MgCl2 and 10 mM L-lysine
Methanocaldococcus jannaschii
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
1,5-Diaminopentane
-
Methanocaldococcus jannaschii
1,6-diaminohexane
-
Methanocaldococcus jannaschii
1,7-Diaminoheptane
-
Methanocaldococcus jannaschii
adipic acid
-
Methanocaldococcus jannaschii
azelaic acid
-
Methanocaldococcus jannaschii
caproic acid
-
Methanocaldococcus jannaschii
Ki Value [mM] (protein specific)
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
0.0024
-
1,6-diaminohexane
-
Methanocaldococcus jannaschii
0.0025
-
1,7-Diaminoheptane
-
Methanocaldococcus jannaschii
0.004
-
1,5-Diaminopentane
-
Methanocaldococcus jannaschii
0.089
-
azelaic acid
-
Methanocaldococcus jannaschii
0.13
-
adipic acid
-
Methanocaldococcus jannaschii
0.21
-
caproic acid
-
Methanocaldococcus jannaschii
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
50000
-
x * 50000, mass spectrometry
Methanocaldococcus jannaschii
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
meso-2,6-Diaminoheptanedioate
Methanocaldococcus jannaschii
last step in L-lysine biosynthesis
L-Lysine + CO2
-
Methanocaldococcus jannaschii
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant DAPDC
Methanocaldococcus jannaschii
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
meso-2,6-Diaminoheptanedioate
-
653897
Methanocaldococcus jannaschii
L-Lysine + CO2
-
653897
Methanocaldococcus jannaschii
?
meso-2,6-Diaminoheptanedioate
last step in L-lysine biosynthesis
653897
Methanocaldococcus jannaschii
L-Lysine + CO2
-
653897
Methanocaldococcus jannaschii
?
Subunits (protein specific)
Subunits
Commentary
Organism
?
x * 50000, mass spectrometry
Methanocaldococcus jannaschii
Other publictions for EC 4.1.1.20
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
747000
Son
Structural basis for substrat ...
Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Biochem. Biophys. Res. Commun.
495
1815-1821
2018
-
-
1
1
6
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1
2
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4
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1
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4
1
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1
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1
1
1
6
-
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1
2
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1
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4
1
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1
1
-
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-
748217
Peverelli
Dimerization of bacterial dia ...
Bacillus anthracis, Bacillus anthracis Sterne, Escherichia coli, Escherichia coli K-12 / MG1655, Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 / H37Rv, Vibrio cholerae serotype O1, Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
J. Biol. Chem.
291
9785-9795
2016
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-
4
-
2
-
-
8
-
-
4
8
-
16
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-
4
-
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16
8
4
-
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4
4
-
-
4
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4
4
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2
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8
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4
8
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4
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-
16
8
4
-
-
4
4
-
-
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-
12
12
-
-
-
747204
Peverelli
An optimized coupled assay fo ...
Bacillus anthracis, Bacillus anthracis Sterne, Escherichia coli, Escherichia coli K-12 / MG1655, Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 / H37Rv, no activity in Homo sapiens
Biochimie
115
78-85
2015
-
-
3
-
-
-
-
3
-
-
-
6
-
15
-
-
3
-
-
-
-
-
12
-
3
-
-
3
3
-
-
3
-
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-
3
3
-
-
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-
-
3
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6
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3
-
-
-
-
12
-
3
-
-
3
3
-
-
-
-
3
3
-
-
-
726639
Oliver
The purification, crystallizat ...
Arabidopsis thaliana
Acta Crystallogr. Sect. F
70
663-668
2014
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1
1
-
-
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1
-
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-
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6
-
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2
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2
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2
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-
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-
714346
Fogle
Analysis of catalytic determin ...
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
Biochim. Biophys. Acta
1814
1113-1119
2011
-
-
-
-
-
-
4
3
-
-
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5
-
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1
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9
-
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4
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1
4
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1
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6
6
3
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1
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-
9
-
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-
5
-
-
-
-
-
-
-
-
3
3
716423
Cheraghi
Improved production of L-lysin ...
Corynebacterium glutamicum, Corynebacterium glutamicum ATC21799
Pak. J. Biol. Sci.
13
504-508
2010
-
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1
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2
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4
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2
1
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1
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1
1
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2
1
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1
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1
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705411
Weyand
The three-dimensional structur ...
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
J. Struct. Funct. Genomics
10
209-217
2009
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1
1
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1
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5
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1
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2
2
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1
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1
1
1
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1
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1
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2
2
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693099
Hu
The catalytic intermediate sta ...
Helicobacter pylori
J. Biol. Chem.
283
21284-21293
2008
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1
1
6
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6
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3
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1
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1
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6
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1
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1
1
1
6
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6
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1
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1
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6
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677889
Kim
-
Diaminopimelate decarboxylase ...
Arabidopsis thaliana
Asian J. Plant Sci.
5
260-265
2006
-
-
1
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-
1
-
1
2
-
2
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5
-
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3
1
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1
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1
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2
2
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1
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1
2
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5
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3
1
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1
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680259
Kim
-
Characterization of a gene enc ...
Oryza sativa
Integr. Biosci.
10
197-201
2006
-
-
1
-
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-
1
-
1
1
-
1
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2
1
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1
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1
1
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1
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1
1
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2
1
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-
663552
Kefala
Cloning, expression, purificat ...
Mycobacterium tuberculosis
Acta Crystallogr. Sect. F
F61
782-784
2005
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-
1
1
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3
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1
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1
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1
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664355
Gunji
Characterization of the L-lysi ...
Methylophilus methylotrophus
Biosci. Biotechnol. Biochem.
68
1449-1460
2004
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-
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4
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2
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-
652392
Gokulan
Crystal structure of Mycobacte ...
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
J. Biol. Chem.
278
18588-18596
2003
-
-
1
1
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2
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7
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1
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2
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1
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649192
Momany
Crystallization of diaminopime ...
Escherichia coli
Acta Crystallogr. Sect. D
58
549-552
2002
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1
1
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2
1
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3
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2
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653897
Ray
Cocrystal structures of diamin ...
Methanocaldococcus jannaschii
Structure
10
1499-1508
2002
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1
1
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6
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1
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2153
Chatterjee
Biosynthesis of lysine in plan ...
Chlamydomonas sp., Glycine max, Nicotiana tabacum, Zea mays
Plant Mol. Biol.
26
285-290
1994
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4
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4128
Mills
Cloning and sequence analysis ...
Bacillus methanolicus
Appl. Environ. Microbiol.
59
2927-2937
1993
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1
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1
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1
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-
4125
Styriak
DAP-decarboxylase activity and ...
Butyrivibrio fibrisolvens, Clostridium spp., Fibrobacter succinogenes, Megasphaera elsdenii, Selenomonas ruminantium, Streptococcus equinus
Arch. Anim. Nutr.
42
71-77
1992
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6
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12
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1
6
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6
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6
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1
6
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6
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4124
Yeh
General organization of the ge ...
Corynebacterium glutamicum
Mol. Gen. Genet.
212
105-111
1988
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1
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4
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2
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4123
Kelland
Analogs of diaminopimelic acid ...
Lysinibacillus sphaericus, Triticum sp.
J. Biol. Chem.
261
13216-13223
1986
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4121
Jouanneau
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Expression in mammalian cells ...
Escherichia coli
Eur. J. Biochem.
145
175-178
1985
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1
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4122
Kelland
Stereochemistry of lysine form ...
Triticum sp.
Biochemistry
24
3263-3267
1985
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4
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4120
Bakhiet
-
Lysine biosynthesis in Methano ...
Methanospirillum hungatei, Methanothermobacter thermautotrophicus
Curr. Microbiol.
10
195-198
1984
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2
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1
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4118
Dierks-Ventling
Lysine biosynthesis and utiliz ...
Zea mays
Planta
157
233-238
1983
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1
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4119
Sen
-
Activity of diaminopimelic aci ...
Arthrobacter globiformis, Corynebacterium glutamicum, Enterococcus faecalis, Kocuria varians, Micrococcus luteus, Staphylococcus aureus
Acta Biotechnol.
3
217-220
1983
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9
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2142
Chatterjee
-
Activities and regulation of t ...
Bacillus megaterium
J. Gen. Microbiol.
128
1073-1081
1982
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4115
Asada
-
Purification and properties of ...
Lysinibacillus sphaericus
Agric. Biol. Chem.
45
1513-1514
1981
2
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4
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4116
Asada
Stereochemistry of meso-'a,e'- ...
Lysinibacillus sphaericus
Biochemistry
20
6881-6886
1981
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4113
Schroder
Lysinbiosynthese bei Pseudomon ...
Pseudomonas aeruginosa
Z. Allg. Mikrobiol.
18
361-364
1978
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4114
Schroeder
Lysinbiosynthese bei Pseudomon ...
Pseudomonas aeruginosa
Z. Allg. Mikrobiol.
18
453-456
1978
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4112
Mazelis
A chloroplast-localized diamin ...
Vicia faba
FEBS Lett.
64
197-200
1976
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2
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4127
White
The regulation of diaminopimel ...
Escherichia coli
J. Gen. Microbiol.
96
51-62
1976
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4111
Rosner
Control of lysine biosynthesis ...
Bacillus subtilis, Brevibacterium sp.
J. Bacteriol.
121
20-28
1975
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1
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4109
Vogel
-
Diaminopimelate decarboxylase ...
Landoltia punctata, Lemna perpusilla
Methods Enzymol.
17B
146-150
1971
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3
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4110
White
-
Diaminopimelate decarboxylase ...
Escherichia coli
Methods Enzymol.
17B
140-145
1971
1
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5
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4108
Denman
Diaminopimelic acid decarboxyl ...
Escherichia coli
Biochim. Biophys. Acta
16
442-443
1955
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