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Information on EC 4.1.1.64 - 2,2-dialkylglycine decarboxylase (pyruvate) and Organism(s) Burkholderia cepacia and UniProt Accession P16932

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.1 Carboxy-lyases
                4.1.1.64 2,2-dialkylglycine decarboxylase (pyruvate)
IUBMB Comments
A pyridoxal-phosphate protein. Acts on 2-amino-2-methylpropanoate (i.e. 2-methylalanine), 2-amino-2-methylbutanoate and 1-aminocyclopentanecarboxylate.
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This record set is specific for:
Burkholderia cepacia
UNIPROT: P16932
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Word Map
The taxonomic range for the selected organisms is: Burkholderia cepacia
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
dialkylglycine decarboxylase, 2,2-dialkylglycine decarboxylase (pyruvate), more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dialkylglycine decarboxylase
-
2,2-Dialkyl-2-amino acid-pyruvate aminotransferase
-
-
-
-
alpha-Dialkyl amino acid transaminase
-
-
-
-
alpha-Dialkylamino acid aminotransferase
-
-
-
-
alpha-Dialkylamino acid transaminase
-
-
-
-
Decarboxylase, dialkyl amino acid (pyruvate)
-
-
-
-
Dialkylamino-acid decarboxylase (pyruvate)
-
-
-
-
dialkylglycine decarboxylase
-
-
L-Alanine-alpha-ketobutyrate aminotransferase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2,2-dialkylglycine + pyruvate = dialkyl ketone + CO2 + L-alanine
show the reaction diagram
2,2-dialkylglycine + pyruvate = dialkyl ketone + CO2 + L-alanine
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
-
-
-
-
transamination
-
-
SYSTEMATIC NAME
IUBMB Comments
2,2-dialkylglycine carboxy-lyase (amino-transferring; L-alanine-forming)
A pyridoxal-phosphate protein. Acts on 2-amino-2-methylpropanoate (i.e. 2-methylalanine), 2-amino-2-methylbutanoate and 1-aminocyclopentanecarboxylate.
CAS REGISTRY NUMBER
COMMENTARY hide
9032-17-1
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2,2-dialkylglycine + pyruvate
dialkyl ketone + CO2 + L-alanine
show the reaction diagram
-
-
-
?
2-Aminoisobutanoate + pyruvate
L-Ala + acetone + CO2
show the reaction diagram
-
-
-
?
1-Amino-1-cyclohexane-carboxylate + pyruvate
L-Ala + ? + CO2
show the reaction diagram
-
-
-
-
?
1-Amino-1-cyclopentane-carboxylate + pyruvate
L-Ala + ? + CO2
show the reaction diagram
-
-
-
-
?
2-Aminoisobutanoate + pyruvate
L-Ala + acetone + CO2
show the reaction diagram
2-aminoisobutyrate + pyruvate
L-Ala + acetone + CO2
show the reaction diagram
alpha-Aminomalonate + pyruvate
Gly + ? + CO2
show the reaction diagram
-
nonoxidative decarboxylation
-
?
alpha-Aminomalonate + pyruvate + O2
Ala + ? + CO2
show the reaction diagram
-
-
-
?
D-Ala + pyruvate
L-Ala + ? + CO2
show the reaction diagram
-
-
-
-
?
Gly + pyruvate
L-Ala + ? + CO2
show the reaction diagram
-
-
-
-
?
Isopropylamine + pyruvate
L-Ala + ? + CO2
show the reaction diagram
-
-
-
-
?
Isovaline + pyruvate
L-Ala + butanone + CO2
show the reaction diagram
-
-
-
-
?
L-Ala + pyruvate
L-Ala + ? + CO2
show the reaction diagram
-
-
-
-
?
L-Phenylglycine + pyruvate
L-Ala + ? + CO2
show the reaction diagram
-
-
-
-
?
Pyruvate + 2-aminoisobutanoate
?
show the reaction diagram
-
-
-
-
?
Pyruvate + Gly
?
show the reaction diagram
-
-
-
-
?
Pyruvate + isopropylamine
?
show the reaction diagram
-
-
-
-
?
Pyruvate + L-Ala
?
show the reaction diagram
-
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2,2-dialkylglycine + pyruvate
dialkyl ketone + CO2 + L-alanine
show the reaction diagram
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
-
pyridoxal 5'-phosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ba2+
-
gives 10fold lower activity compared to monovalent alkali cations of similar ionic radius, increases association of pyridoxal 5'-phosphate and decreases dissociation rate constant of pyridoxal 5'-phosphate
Ca2+
-
gives 10fold lower activity compared to monovalent alkali cations of similar ionic radius
Cs+
-
activates to a lesser extent than K+
Li+
-
activates to a lesser extent than K+
Mg2+
-
gives 10fold lower activity compared to monovalent alkali cations of similar ionic radius
Na+
-
activates to a lesser extent than K+, increases association of pyridoxal 5'-phosphate and decreases dissociation rate constant of pyridoxal 5'-phosphate
Tl+
-
activates to a lesser extent than K+
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(R)-1-amino-1-methylpropanephosphonate
-
(R)-1-amino-1-phenylethanephosphonate
-
(R)-1-aminoethanephosphonate
-
(S)-1-aminoethanephosphonate
-
1-amino-1-cyclopropane carboxylate
i.e. ACC
1-aminocyclopentanephosphonate
-
5'-phosphopyridoxyl-2-methylalanine
i.e. PPL-MeAla
D-cycloserine
competitive, L-isomer has 3000fold greater inhibitory potency than D-isomer
L-Cycloserine
competitive, L-isomer has 3000fold greater inhibitory potency than D-isomer
phosphono-2-methylalanine
-
1-aminocyclopropane 1-carboxylate
-
-
3,3,3-Trifluoro-2-aminoisobutanoate
-
irreversible, the inhibitor undergoes catalytic decarboxylation during the inactivation process and binds at the enzyme's active site
D-cycloserine
-
-
Gly
-
competitive against 2-aminoisobutanoate
L-Cycloserine
-
-
pyruvate
-
-
additional information
-
not inhibitory: pyruvate
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
30
2-aminoisobutanoate
pH 7.8, mutant enzyme Q52A
0.015
pyruvate
pH 7.8, mutant enzyme Q52A
1.12 - 66
2-aminoisobutanoate
2.2
2-aminoisobutyrate
-
pH 7.5
0.098 - 0.17
pyruvate
additional information
additional information
-
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.12
2-aminoisobutanoate
pH 7.8, mutant enzyme Q52A
0.12
pyruvate
pH 7.8, mutant enzyme Q52A
2.3
1-amino-1-cyclohexanecarboxylate
-
with pyruvate as cosubstrate, decarboxylation
0.98
1-amino-1-cyclopentanecarboxylate
-
with pyruvate as cosubstrate, decarboxylation
0.05 - 25
2-aminoisobutanoate
0.025
alpha-aminomalonate
-
with pyruvate as cosubstrate, oxidative decarboxylation
0.2
D-Ala
-
with pyruvate as cosubstrate, decarboxylation
0.0012
Gly
-
with pyruvate as cosubstrate, decarboxylation
0.033
L-Ala
-
with pyruvate as cosubstrate, decarboxylation
additional information
additional information
-
-
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4.9
(R)-1-amino-1-methylpropanephosphonate
pH 7.8, homologous to L-isovaline
13
(R)-1-amino-1-phenylethanephosphonate
pH 7.8, homologous to L-phenylglycine
19
(R)-1-aminoethanephosphonate
pH 7.8, homologous to L-alanine
1.1
(S)-1-aminoethanephosphonate
pH 7.8, homologous to D-alanine
6
1-aminocyclopentanephosphonate
pH 7.8, homologous to aminocyclopropane carboxylate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
pH-dependence of transamination half-reaction
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
DGDA_BURCE
433
0
46444
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
46500
4 * 46500, alpha4, calculation from crystallographic data
188000
-
equilibrium sedimentation
46500
-
4 * 46500, SDS-PAGE
47000
-
4 * 47000, ultracentrifugal analysis in presence of 8 M urea or 7 M guanidine HCl
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
4 * 46500, alpha4, calculation from crystallographic data
tetramer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, crystal structure of Q52A mutant and wild-type enzyme in complex with pyridoxamine 5'-phosphate
in complex with different aminophosphonate inhibitors
in complex with four inhibitors
crystal structure at 2.8 A resolution of tzhe enzyme with Li+ or Rb+ bound
-
crystal structures at 2.8 A resolution with Li+ and Rb+ bound at the binding site for alkali metal ions which is close to the active site, i.e. site 1
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Q52A
85fold decrease in turnover number for decarboxylation half-reaction with 2-aminoisobutyrate and pyruvate, greatly reduced rate of transamination half-reaction and impaired pyridoxamine phosphate binding
Q52E
10000fold decrease in turnover number for decarboxylation half-reaction with 2-aminoisobutyrate and pyruvate, transamination rate is nearly identical to wild-type value
Q52I
100000fold decrease in turnover number for decarboxylation half-reaction with 2-aminoisobutyrate and pyruvate, greatly reduced rate of transamination half-reaction and impaired pyridoxamine phosphate binding
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Keller, J.W.; O'Leary, M.H.
3,3,3-Trifluoro-2-aminoisobutyrate: a mechanism-based inhibitor of Pseudomonas cepacia alpha-dialkylamino acid
Biochem. Biophys. Res. Commun.
90
1104-1110
1979
Burkholderia cepacia
Manually annotated by BRENDA team
Lamatiniere, C.A.; Itho, H.; Dempsey, W.B.
alpha-Dialkyl acid transaminase from Pseudomonas cepacia. Purification, crystallization, physical, and kinetic properties
Biochemistry
10
4783-4788
1971
Burkholderia cepacia
Manually annotated by BRENDA team
Hohenester, E.; Keller, J.W.; Jansonius, J.N.
An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase
Biochemistry
33
13561-13570
1994
Burkholderia cepacia
Manually annotated by BRENDA team
Zhou, X.; Kay, S.; Toney, M.D.
Coexisting kinetically distinguishable forms of dialkylglycine decarboxylase engendered by alkali metal ions
Biochemistry
37
5761-5769
1998
Burkholderia cepacia
Manually annotated by BRENDA team
Sun, S.; Zabinski, R.F.; Toney, M.D.
Reactions of alternate substrates demonstrate stereoelectronic control of reactivity in dialkylglycine decarboxylase
Biochemistry
37
3865-3875
1998
Burkholderia cepacia
Manually annotated by BRENDA team
Sun, S.; Bagdassarian, C.K.; Toney, M.D.
Pre-steady-state kinetic analysis of the reactions of alternate substrates with dialkylglycine decarboxylase
Biochemistry
37
3876-3885
1998
Burkholderia cepacia
Manually annotated by BRENDA team
Zhou, X.; Toney, M.D.
pH Studies on the mechanism of the pyridoxal phosphate-dependent dialkylglycine decarboxylase
Biochemistry
38
311-320
1999
Burkholderia cepacia
Manually annotated by BRENDA team
Toney, M.D.; Hohenester, E.; Keller, J.W.; Jansonius, J.N.
Structural and mechanistic analysis of two refined crystal structures of the pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase
J. Mol. Biol.
245
151-179
1995
Burkholderia cepacia (P16932)
Manually annotated by BRENDA team
Keller, J.W.; Baurick, K.B.; Rutt., G.C.; O'Malley, M.V.; Sonafrank, N.L.; Reynolds, R.A.; Ebbesson, L.O.E.; Vajdos, F.F.
Pseudomonas cepacia 2,2-dialkylglycine decarboxylase
J. Biol. Chem.
265
5531-5539
1990
Burkholderia cepacia
Manually annotated by BRENDA team
Zhou, X.; Jin, X.; Medhekar, R.; Chen, X.; Dieckmann, T.; Toney, M.D.
Rapid kinetic and isotopic studies on dialkylglycine decarboxylase
Biochemistry
40
1367-1377
2001
Burkholderia cepacia
Manually annotated by BRENDA team
Liu, W.; Rogers, C.J.; Fisher, A.J.; Toney, M.D.
Aminophosphonate inhibitors of dialkylglycine decarboxylase: structural basis for slow binding inhibition
Biochemistry
41
12320-12328
2002
Burkholderia cepacia (P16932)
Manually annotated by BRENDA team
Malashkevich, V.N.; Strop, P.; Keller, J.W.; Jansonius, J.N.; Toney, M.D.
Crystal structures of dialkylglycine decarboxylase inhibitor complexes
J. Mol. Biol.
294
193-200
1999
Burkholderia cepacia (P16932)
Manually annotated by BRENDA team
Liu, W.; Toney, M.D.
Kinetic and thermodynamic analysis of the interaction of cations with dialkylglycine decarboxylase
Biochemistry
43
4998-5010
2004
Burkholderia cepacia
Manually annotated by BRENDA team
Fogle, E.J.; Liu, W.; Woon, S.T.; Keller, J.W.; Toney, M.D.
Role of Q52 in catalysis of decarboxylation and transamination in dialkylglycine decarboxylase
Biochemistry
44
16392-16404
2005
Burkholderia cepacia (P16932)
Manually annotated by BRENDA team
Schnackerz, K.D.; Keller, J.; Phillips, R.S.; Toney, M.D.
Ionization state of pyridoxal 5'-phosphate in d-serine dehydratase, dialkylglycine decarboxylase and tyrosine phenol-lyase and the influence of monovalent cations as inferred by (31)P NMR spectroscopy
Biochim. Biophys. Acta
1764
230-238
2006
Burkholderia cepacia
Manually annotated by BRENDA team
Bassyouni, F.A.; Saleh, T.S.; ElHefnawi, M.M.; Abd El-Moez, S.I.; El-Senousy, W.M.; Abdel-Rehim, M.E.
Synthesis, pharmacological activity evaluation and molecular modeling of new polynuclear heterocyclic compounds containing benzimidazole derivatives
Arch. Pharm. Res.
35
2063-2075
2012
Burkholderia cepacia (P16932)
Manually annotated by BRENDA team