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Information on EC 4.2.99.21 - isochorismate lyase and Organism(s) Pseudomonas aeruginosa and UniProt Accession Q51507

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EC Tree
     4 Lyases
         4.2 Carbon-oxygen lyases
             4.2.99 Other carbon-oxygen lyases
                4.2.99.21 isochorismate lyase
IUBMB Comments
This enzyme is part of the pathway of salicylate formation from chorismate, and forms an integral part of pathways that produce salicylate-derived siderophores, such as pyochelin and yersiniabactin.
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This record set is specific for:
Pseudomonas aeruginosa
UNIPROT: Q51507
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Word Map
The taxonomic range for the selected organisms is: Pseudomonas aeruginosa
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
isochorismate pyruvate lyase, isochorismate-pyruvate lyase, isochorismate lyase, prxr1, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isochorismate-pyruvate lyase
-
pyochelin biosynthetic protein PchB
-
-
-
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isochorismate pyruvate lyase
isochorismate-pyruvate lyase
-
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salicylate biosynthesis protein pchB
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-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
isochorismate = salicylate + pyruvate
show the reaction diagram
the enzyme achieves catalysis of both pericyclic reactions, isochorismate-pyruvate lyase and chorismate-pyruvate lyase, EC 4.1.3.40, in part by the stabilization of reactive conformations and in part by electrostatic transition-state stabilization. Both, substrate organization and electrostatic transition state stabilization, contribute to catalysis
isochorismate = salicylate + pyruvate
show the reaction diagram
SYSTEMATIC NAME
IUBMB Comments
isochorismate pyruvate-lyase (salicylate-forming)
This enzyme is part of the pathway of salicylate formation from chorismate, and forms an integral part of pathways that produce salicylate-derived siderophores, such as pyochelin and yersiniabactin.
CAS REGISTRY NUMBER
COMMENTARY hide
383896-77-3
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
isochorismate
salicylate + pyruvate
show the reaction diagram
isochorismate
salicylate + pyruvate
show the reaction diagram
additional information
?
-
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
isochorismate
salicylate + pyruvate
show the reaction diagram
-
-
-
?
isochorismate
salicylate + pyruvate
show the reaction diagram
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
no cofactor required
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
no metal cofactor requirement
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(4R,5R)-5-[(1-carboxyethenyl)oxy]-4-hydroxycyclohex-1-ene-1-carboxylic acid
inhibition of salicylate synthase activity
4,4'-sulfonylbis(2,6-dinitrophenol)
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4,6-dinitro-2-oxo-1,3-benzoxathiol-5-yl methyl carbonate
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5-[(2-carboxyphenyl)sulfamoyl]-2-hydroxybenzoic acid
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additional information
-
not inhibitory at 1 mM: EDTA, EGTA, or o-phenanthroline. No substrate inhibition up to 1.2 mM
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00079 - 0.134
isochorismate
additional information
additional information
-
Michaelis-Menten kinetics and thermodynamics, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00038 - 1.76
isochorismate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.017 - 1130
isochorismate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.16
(4R,5R)-5-[(1-carboxyethenyl)oxy]-4-hydroxycyclohex-1-ene-1-carboxylic acid
pH and temperature not specified in the publication, inhibition of salicylate synthase activity
0.0001
4,4'-sulfonylbis(2,6-dinitrophenol)
pH and temperature not specified in the publication
0.00087
4,6-dinitro-2-oxo-1,3-benzoxathiol-5-yl methyl carbonate
pH and temperature not specified in the publication
0.0001
5-[(2-carboxyphenyl)sulfamoyl]-2-hydroxybenzoic acid
pH and temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
12.89
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pH 7.0, 37°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 9
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
the first committed step during the biosynthesis of siderophores, which are small molecules capable of chelating iron from the host organism, is the conversion of chorismate into isochorismate by isochorismate synthase (EC 5.4.4.2) and consequently to salicylate by isochorismate pyruvate-lyase (EC 4.2.99.21). Salicylate synthase converts chorismate into salicylate through a two-step reaction
physiological function
the enzyme is involved in the biosynthesis of pyochelin. Chorismate-utilizing enzymes (CUE) such as chorismate mutase, anthranilate synthase, chorismate pyruvate-lyase, 4-amino-4-deoxychorismate synthase, isochorismate synthase and salicylate synthase are responsible for converting chorismate into various products necessary for the survival of bacteria
evolution
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PchB is a structural homologue of the AroQ chorismate mutases
metabolism
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the enzyme is involved in siderophore pyochelin via salicylate biosynthesis
physiological function
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the enzyme physiologically catalyzes the elimination of the enolpyruvyl side chain from isochorismate to make salicylate for incorporation into the siderophore pyochelin
additional information
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structure-function relationship, biocatalysis of pericyclic reactions, overview. For PchB, the pericyclic reaction is a concerted but asynchronous [1,5]-sigmatropic shift with a quantitative transfer of hydrogen from C2 to C9. Major structural difference between the apo form and the pyruvate-bound or the pyruvate-and salicylate-bound forms of PchB: the active site loop between helix 1 and helix 2 is disordered in the apo structure but fully ordered in the ligand-bound structures. The difference between the open and closed structures is due to a conserved active site lysine 42, which hydrogen bonds to a bound pyruvate molecule. Quantum mechanical/molecular mechanical molecular dynamics simulations, overview
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
11563
x * 11563, calculated
11500
-
2 * 14000, SDS-PAGE, 2 * 11500, calculated
14000
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2 * 14000, SDS-PAGE, 2 * 11500, calculated
31000 - 34000
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gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 11563, calculated
dimer
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2 * 14000, SDS-PAGE, 2 * 11500, calculated
additional information
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enzyme is an intertwined dimer of three helices with connecting loops, and amino acids from each monomer participate in each of two active sites, crystallization data
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged wild-type enzyme and mutant K42E in complex with salicylate and pyruvate, hanging drop vapor diffusion method, mixing of 0.001 ml of 64 mg/ml wild-type protein with 0.001 ml of reservoir solution containing 0.2 M lithium sulfate, 0.1 M sodium acetate, pH 4.5, and 6% glycerol, mixing of 0.001 ml of 34 mg/ml mutant protein with 0.001 ml reservoir solution containing 0.004 M Gly-Gly, 0.100 M sodium acetate, pH 3.6, and 12% glycerol, ligands in 20fold molar excess, 25°C, 24-48 h, X-ray diffraction structure determination and analysis, modeling
wild-type and mutant K42E, to 1.95 and 1.79 A resolution, respectively, in complex with salicylate and pyruvate
apo-structure, to 2.35 A resolution, has one dimer per asymmetric unit with nitrate bound in an open active site. The loop between the first and second helices is disordered, providing a gateway for substrate entry and product exit. The pyruvate-bound structure, to 1.95 A resolution, has two dimers per asymmetric unit. One has two open active sites like the apo structure, and the other has two closed active sites with the loop between the first and second helices ordered for catalysis
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molecular dynamics simulations and averaged intermolecular substrate-protein distances, active-site volumes for reactants and transition state
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X-ray crystallographic structures for mutant K42A with salicylate and pyruvate bound, to 2.5 A resolution, and for apo-I87T, to 2.15 A resolution. Circular dichroism studies of mutants K42A, K42Q, K42E, and K42H, A43P and I87T
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A375T
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loss of the physiological isochorismate synthase catalytic efficiency by three orders of magnitude, and a 2fold gain in isochorismate-pyruvate lyase catalytic efficiency
A37I
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mutation increases the rate constant for the chorismate mutase activity by a factor of 1000, and also increases the isochorismate pyruvate lyase catalytic efficiency, by a factor of 6
A43P
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about 25% decrease in both chorismate mutase and isochorismate pyruvate lyase activity
C7A
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mutant has a reduced catalytic free energy of activation of up to 0.17 kcal/mol
C7A/K42C
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mutant has a reduced catalytic free energy of activation of up to 4.2 kcal/mol. Treatment with bromoethylamine leads to 64% recovery of activity
D310E
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physiological isochorismate synthase catalytic efficiency similar to wild-type, 3fold gain in isochorismate-pyruvate lyase catalytic efficiency
D310E/A375T
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similar activity in the isochorismate synthase and isochorismate-pyruvate lyase assays as the A375T variant
I87T
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structure demonstrates considerable mobility, decrease in both chorismate mutase and isochorismate pyruvate lyase activity
I88T
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no isochorismate pyruvate lyase activity, retains chorismate mutase activity
K42C
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mutant has a reduced catalytic free energy of activation of up to 4.4 kcal/mol. Treatment with bromoethylamine leads to 55% recovery of activity
K42E
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almost complete loss of activity
K42H
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strong decrease in activity
K42Q
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almost complete loss of activity
Q91N
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20fold decrease in both isochorismate pyruvate lyase and chorismate mutase activity
R54K
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100fold decrease in both isochorismate pyruvate lyase and chorismate mutase activity
additional information
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a CM-deficient Escherichia coli mutant, which is auxotrophic for phenylalanine and tyrosine, is functionally complemented by the cloned pchB gene for growth in minimal medium
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
sequence comparisons
expression in Escherichia coli
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expression of a fusion of genes pchA and pchB from Pseudomonas aeruginosa, which encode isochorismate synthase and isochorismate pyruvate-lyase, in Arabidopsis thaliana
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
an entB mutant of Escherichia coli blocked in the conversion of isochorismate to 2,3-dihydro-2,3-dihydroxybenzoate forms salicylate when transformed with a pchB expression construct. Salicylate formation occurs in vitro when chorismate is incubated with a crude extract of Pseudomons aeruginosa containing overproduced PchA and PchB proteins, salicylate and pyruvate are formed in equimolar amounts
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
agriculture
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expression of a fusion of genes pchA and pchB from Pseudomonas aeruginosa, which encode isochorismate synthase and isochorismate pyruvate-lyase, in Arabidopsis thaliana, with targeting of the gene product either to the cytosol, c-SAS plants, or to the chloroplast, p-SAS plants. In p-SAS plants, the amount of free and conjugated SA is increased more than 20fold above wild type level. P-SAS plants show a strongly dwarfed phenotype and produce very few seeds. Targeting of SAS to the cytosol causes a slight increase in free salicylic acid and a significant threefold increase in conjugated salicylic acid. The modest increase in total salicylic content does not strongly induce the resistance marker PR-1, but results in enhanced disease resistance towards a virulent isolate of Peronospora parasitica. Increased resistance of c-SAS lines is paralleled with reduced seed production
biotechnology
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alternative computational rational approach to improve the secondary catalytic activity of enzymes, taking as a test case the IPL enzyme. The approach is based on the use of molecular dynamic simulations employing hybrid quantum mechanics/molecular mechanics methods that allow describing breaking and forming bonds
synthesis
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alternative computational rational approach to improve the secondary catalytic activity of enzymes, taking as a test case the IPL enzyme. The approach is based on the use of molecular dynamic simulations employing hybrid quantum mechanics/molecular mechanics methods that allow describing breaking and forming bonds
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kunzler, D.E.; Sasso, S.; Gamper, M.; Hilvert, D.; Kast, P.
Mechanistic insights into the isochorismate pyruvate lyase activity of the catalytically promiscuous PchB from combinatorial mutagenesis and selection
J. Biol. Chem.
280
32827-32834
2005
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Luo, Q.; Olucha, J.; Lamb, A.L.
Structure-function analyses of isochorismate-pyruvate lyase from Pseudomonas aeruginosa suggest differing catalytic mechanisms for the two pericyclic reactions of this bifunctional enzyme
Biochemistry
48
5239-5245
2009
Pseudomonas aeruginosa
Manually annotated by BRENDA team
DeClue, M.S.; Baldridge, K.K.; Kunzler, D.E.; Kast, P.; Hilvert, D.
Isochorismate pyruvate lyase: a pericyclic reaction mechanism?
J. Am. Chem. Soc.
127
15002-15003
2005
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Marti, S.; Andres, J.; Moliner, V.; Silla, E.; Tunon, I.; Bertran, J.
Predicting an improvement of secondary catalytic activity of promiscuous isochorismate pyruvate lyase by computational design
J. Am. Chem. Soc.
130
2894-2895
2008
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Marti, S.; Andres, J.; Moliner, V.; Silla, E.; Tunon, I.; Bertran, J.
Mechanism and plasticity of isochorismate pyruvate lyase: a computational study
J. Am. Chem. Soc.
131
16156-16161
2009
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Gaille, C.; Kast, P.; Haas, D.
Salicylate biosynthesis in Pseudomonas aeruginosa. Purification and characterization of PchB, a novel bifunctional enzyme displaying isochorismate pyruvate-lyase and chorismate mutase activities
J. Biol. Chem.
277
21768-21775
2002
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Zaitseva, J.; Lu, J.; Olechoski, K.L.; Lamb, A.L.
Two crystal structures of the isochorismate pyruvate lyase from Pseudomonas aeruginosa
J. Biol. Chem.
281
33441-33449
2006
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Serino, L.; Reimmann, C.; Baur, H.; Beyeler, M.; Visca, P.; Haas, D.
Structural genes for salicylate biosynthesis from chorismate in Pseudomonas aeruginosa
Mol. Gen. Genet.
249
217-228
1995
Pseudomonas aeruginosa (Q51507)
Manually annotated by BRENDA team
Mauch, F.; Mauch-Mani, B.; Gaille, C.; Kull, B.; Haas, D.; Reimmann, C.
Manipulation of salicylate content in Arabidopsis thaliana by the expression of an engineered bacterial salicylate synthase
Plant J.
25
67-77
2001
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Olucha, J.; Ouellette, A.N.; Luo, Q.; Lamb, A.L.
pH Dependence of catalysis by Pseudomonas aeruginosa isochorismate-pyruvate lyase: implications for transition state stabilization and the role of lysine 42
Biochemistry
50
7198-7207
2011
Pseudomonas aeruginosa (Q51507), Pseudomonas aeruginosa
Manually annotated by BRENDA team
Luo, Q.; Meneely, K.M.; Lamb, A.L.
Entropic and enthalpic components of catalysis in the mutase and lyase activities of Pseudomonas aeruginosa PchB
J. Am. Chem. Soc.
133
7229-7233
2011
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Lamb, A.L.
Pericyclic reactions catalyzed by chorismate-utilizing enzymes
Biochemistry
50
7476-7483
2011
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Choutko, A.; Eichenberger, A.P.; van Gunsteren, W.F.; Dolenc, J.
Exploration of swapping enzymatic function between two proteins: a simulation study of chorismate mutase and isochorismate pyruvate lyase
Protein Sci.
22
809-822
2013
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Meneely, K.M.; Luo, Q.; Lamb, A.L.
Redesign of MST enzymes to target lyase activity instead promotes mutase and dehydratase activities
Arch. Biochem. Biophys.
539
70-80
2013
Pseudomonas aeruginosa, Yersinia enterocolitica (Q9X9I8), Yersinia enterocolitica ATCC 33114 (Q9X9I8)
Manually annotated by BRENDA team
Olucha, J.; Meneely, K.M.; Lamb, A.L.
Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB
Biochemistry
51
7525-7532
2012
Pseudomonas aeruginosa
Manually annotated by BRENDA team
Svarcova, M.; Kratky, M.; Vinsova, J.
Investigation of potential inhibitors of chorismate-utilizing enzymes
Curr. Med. Chem.
22
1383-1399
2015
Mycobacterium tuberculosis (P9WFX1), Mycobacterium tuberculosis ATCC 25618 (P9WFX1), no activity in Homo sapiens, Pseudomonas aeruginosa (Q51507), Pseudomonas aeruginosa ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 (Q51507), Yersinia enterocolitica, Yersinia pestis
Manually annotated by BRENDA team