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Enzyme Nomenclature
Information on EC 4.1.3.38 - aminodeoxychorismate lyase
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
topEC NUMBER 
COMMENTARY 
4.1.3.38
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RECOMMENDED NAME
GeneOntology No.
aminodeoxychorismate lyase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
4-amino-4-deoxychorismate = 4-aminobenzoate + pyruvate
A pyridoxal-phosphate protein; A pyridoxal-phosphate protein.; a pyridoxal-phosphate protein. Forms part of the folate biosynthesis pathway. Acts on 4-amino-4-deoxychorismate, the product of EC 6.3.5.8, aminodeoxychorismate synthase, to form p-aminobenzoate
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4-amino-4-deoxychorismate = 4-aminobenzoate + pyruvate
catalytic mechanism, overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
beta-elimination
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
SYSTEMATIC NAME
IUBMB Comments
4-amino-4-deoxychorismate pyruvate-lyase (4-aminobenzoate-forming)
A pyridoxal-phosphate protein. Forms part of the folate biosynthesis pathway. Acts on 4-amino-4-deoxychorismate, the product of EC 2.6.1.85, aminodeoxychorismate synthase, to form p-aminobenzoate.
CAS REGISTRY NUMBER
COMMENTARY
132264-33-6
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
plasmodial gene PF14_0557 encodes a functional ADCL; gene PF14_0557
UniProt
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
physiological function
the enzyme is active in folate biosynthesis and essential for the cell growth of the pathogen
additional information
evolution
4-amino-4-deoxychorismate lyases can be divided into two classes of dimeric and monomeric enzyme, respectively
evolution
structure comparisons with related enzymes, overview. PabC enzymes can be classified into two groups depending upon whether an active site and structurally conserved tyrosine is provided from the polypeptide that mainly forms an active site or from the partner subunit in the dimeric assembly
additional information
the catalytic residue Lys251 covalently binds the cofactor pyridoxal 5'-phosphate
additional information
structure-activity relationship of PabC, ligand binding modeling and reaction mechanism, overview. No structure of PabC in complex with ligands is achieved, but a computational model of the catalytic intermediate docked into the enzyme active site is generated. A conserved tyrosine helps to create a hydrophobic wall on one side of the active site that provides important interactions to bind the catalytic intermediate, but it does not appear to participate in interactions with the C atom that undergoes an sp2 to sp3 conversion as pyruvate is produced. An active site threonine hydroxyl contributes a proton used in the reduction of the substrate methylene to pyruvate methyl in the final stage of the mechanism
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-alanine + pyridoxal 5'-phosphate
pyridoxamine 5'-phosphate + pyruvate
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L-alanine and other D- and L-amino acids tested are inert as substrates of transamination
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r
4-amino-4-deoxychorismate
4-aminobenzoate + pyruvate
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last step of the 4-aminobenzoate branch
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?
4-amino-4-deoxychorismate
4-aminobenzoate + pyruvate
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re-face specificity
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?
4-amino-4-deoxychorismate
4-aminobenzoate + pyruvate
the enzyme catalyzes the beta-elimination of pyruvate and the aromatization of the ADC ring to yield 4-aminobenzoate. Substrate synthesis from chorismate and ammonia by chorismate aminase in a coupled assay, the substrate is unstable
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?
4-amino-4-deoxychorismate
4-aminobenzoate + pyruvate
molecular modeling of the catalytic intermediate, overview
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-
?
4-amino-4-deoxychorismate
4-aminobenzoate + pyruvate
simulation and validation of the substrate-binding model, overview
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-
?
4-amino-4-deoxychorismate
4-aminobenzoate + pyruvate
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last step of the 4-aminobenzoate branch
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-
?
additional information
?
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The enzyme shows some transaminase activity towards different D-amino acids (D-Asp, D-Ala and D-Glu, in particular) using 2-oxoacids such as oxaloacetate or pyruvate as amino group acceptors. This activity corresponds to EC 2.6.1.21.
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additional information
?
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The enzyme shows some transaminase activity towards different D-amino acids (D-Asp, D-Ala and D-Glu, in particular) using 2-oxoacids such as oxaloacetate or pyruvate as amino group acceptors. This activity corresponds to EC 2.6.1.21.
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-alanine + pyridoxal 5'-phosphate
pyridoxamine 5'-phosphate + pyruvate
-
L-alanine and other D- and L-amino acids tested are inert as substrates of transamination
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r
4-amino-4-deoxychorismate
4-aminobenzoate + pyruvate
-
last step of the 4-aminobenzoate branch
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-
?
4-amino-4-deoxychorismate
4-aminobenzoate + pyruvate
-
last step of the 4-aminobenzoate branch
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
dependent on, one molecule of cofactor is deeply buried in the cleft between domains I and II, pyridoxal 5'-phosphate adopts the re-face specificity facing the protein side and is covalently linked to the catalytic residue Lys251 by forming an internal aldimine bond, Schiff base linkage
pyridoxal 5'-phosphate
dependent on, the PLP methyl group makes van der Waals interactions with Gln147 and is positioned 3.2 A distant from the carbonyl oxygen of Val175, Ser237 interacts with the pyridoxal 5'-phosphate phosphate
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
D-glutamate
D-Glu (in the absence of 2-oxoacids) inhibits the aminodeoxychorismate lyase activity of the enzyme
additional information
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no feedback inhibition by physiological concentrations of 4-aminobenzoate, its glucose ester, or folates
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
dimer
sequence comparisons, structure modeling of the catalytic intermediate and ligand-bound enzyme, overview
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
small yellow prisms crystals in the unliganded form obtained using the sparse-matrix method along with the hanging-drop vapor-difussion method
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purified recombinant detagged enzyme, hanging drop vapour diffusion method, mixing of 0.001 ml of 33 mg/mL prrotein in 100 mM HEPES, pH 7.5, 500 mM NaCl, 0.1 mM pyridoxal 5'-phosphate, and 10 mM 4-aminobenzoate, with 0001 ml of reservoir solution containing 10% w/v PEG 400, 1.8 M ammonium sulfate and 100 mM MES, pH 6.5, 20°C, 1 week, X-ray diffraction structure dtermination and analysis at 1.75 A resolution
purified recombinant selenomethionine-labeled enzyme and of purified recombinant wild-type enzyme in complex with cofactor pyridoxal 5'-phosphate, hanging drop vapor diffusion method, mixing of 0.001 ml of 10 mg/ml protein in 100 mM NaCl, 20 mM Tris-Cl, pH 8.0, with an equal volume of reservoir solution containing 20% w/v PEG monomethyl ether 5000, 0.1 M Bis-Tris, pH 6.2, 1-2 days to 1 week, 16°C, X-ray diffraction structure determination and analysis at 1.90-2.20 A resolution
sitting drop vapor diffusion method, using 0.1 M HEPES buffer pH 8.0 containing 1.3 M Li2SO4 and 2% (v/v) PEG 200
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DEAE-Sephacel, phenyl-Sepharose column, Superose 6 gel filtration column, Mono Q, Superose 12 column, yield 400-800fold
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fractionation with ammonium sulfate pH 7.5, DEAE-Sephacel column, butyl-Sepharose 4B column, Gigapite column
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fractionation with ammonium sulfate, DEAE-Toyopearl column, butyl-Toyopearl column and Mono Q column
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nickel affinity column chromatography; nickel affinity column chromatography
reactive yellow 3-agarose column, Mono Q HR 5/5 FPLC column, Superose 12HR 10/30 FPLC column, Mono Q HR 5/20 FPLC column, Aquapore RP-300 C8 HPLC column: 4100fold to near homogeneity
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recombinant His-tagged wild-type and selenomethionine-labeled enzymes from Escherichia coli strain BL21(DE3) and B834(DE3), respectively, by nickel affinity chromatography
recombinant His6-tagged enzyme from Escherichia coli by metal affinity chromatography
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) GOLD by nickel affinity chromatography, cleavage of the tag by TEV protease, and gel filtration
Resource ISO column chromatography, ammonium sulfate precipitation, Resource Q column chromatography, and Superdex 75 gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cDNAs are shown to encode functional enzymes by complementation of an Escherichia coli pabC mutant, and by demonstrating that the partially purified recombinant proteins convert 4-amino-4-deoxychorismate to 4-aminobenzoate
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cDNAs are shown to encode functional enzymes by complementation of an Escherichia coli pabC mutant, and by demonstrating that the partially purified recombinant proteins convert 4-amino-4-deoxychorismate to 4-aminobenzoate. The full-length Arabidopsis ADC lyase polypeptide is translocated into isolated pea chloroplasts and, when fused to green fluorescent protein, directed the passenger protein to Arabidopsis chloroplasts in transient expression experiments
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expressed in Escherichia coli BL21(DE3) cells; expressed in Escherichia coli BL21(DE3) cells
gene pabC, expression of His6-tagged enzyme with TEV protease cleavage site in Escherichia coli strain BL21(DE3) GOLD
gene PF14_0557, functional overexpression as His6-tagged protein in Escherichia coli cells
recombinant expression of His-tagged wild-type and selenomethionine-labeled enzymes in Escherichia coli strain BL21(DE3) and B834(DE3), respectively
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K180A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
T30A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
additional information
additional information
a mutant with pabC-1 inactivated still retains about 20% of the wild type level of antibiotic FR-008 production, pabC-1/pabC-2 double mutation severely reduces antibiotic FR-008 production and renders the mutant p-aminobenzoic acid-auxotrophic; pabC-1/pabC-2 double mutation severely reduces antibiotic FR-008 production and renders the mutant p-aminobenzoic acid-auxotrophic
additional information
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a mutant with pabC-1 inactivated still retains about 20% of the wild type level of antibiotic FR-008 production, pabC-1/pabC-2 double mutation severely reduces antibiotic FR-008 production and renders the mutant p-aminobenzoic acid-auxotrophic; pabC-1/pabC-2 double mutation severely reduces antibiotic FR-008 production and renders the mutant p-aminobenzoic acid-auxotrophic
additional information
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a mutant with pabC-1 inactivated still retains about 20% of the wild type level of antibiotic FR-008 production, pabC-1/pabC-2 double mutation severely reduces antibiotic FR-008 production and renders the mutant p-aminobenzoic acid-auxotrophic; pabC-1/pabC-2 double mutation severely reduces antibiotic FR-008 production and renders the mutant p-aminobenzoic acid-auxotrophic
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
the absence of the enzyme in humans and its essentiality in various microbes suggests that inhibition of PabC offers the possibility of therapeutics targeting a range of microbial infections, potential of this protein for early stage drug discovery
LINKS TO OTHER DATABASES (specific for EC-Number 4.1.3.38)
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