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.
The taxonomic range for the selected organisms is: Pseudomonas aeruginosa The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
isochorismate = salicylate + pyruvate
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
[1,5]-sigmatropic reaction mechanism that invokes electrostatic catalysis in analogy to the [3,3]-pericyclic rearrangement of chorismate in chorismate mutase
a reactive substrate conformation is formed upon loop closure of the active site and ordering of the loop contributes to the entropic penalty for converting the enzyme substrate complex to the transition state. The thermodynamic parameters of the physiological lyase activity of PchB show that the reaction is clearly enthalpically driven, and has a very large entropic penalty of 24.3 cal/(mol K), which is more than 1.5-fold greater than that of the uncatalyzed reaction of 15.77 cal/(mol K)
reaction mechanism, the IPL reaction is a concerted but asynchronous hydrogen transfer, by a proposed [1,5]-sigmatropic reaction mechanism with a pericyclic transition state, quantum mechanical/molecular-mechanical calculations and simulations, overview
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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.
pericyclic reaction, elimination of pyruvate. The electrostatic field due to PchB at atoms of isochorismate favors the isochorismate to salicylate transition, molecular dynamics simulations, overview
enzyme additionally catalyzes the rearrangement of chorismate into prephenate and shows chorismate mutase activity. Both transformation of isochorismate into pyruvate and salicylate and the rearrangement of chorismate into prephenate proceed via a pericyclic reaction mechanism
the 2H kinetic isotope effects on kcat and the ratio kcat/Km are 2.34 and 1.75, respectively. Chemistry is significantly rate-determining for the enzyme. The magnitude of the isotope effect is consistent with considerable C-H bond cleavage in the transition state. The significant 2H kinetic isotope effect and quantitative transfer of the label to pyruvate are both consistent with a pericyclic reaction mechanism
PchB possesses weak chorismate mutase activity as well and is able to catalyze two distinct pericyclic reactions in a single active site. The enzyme tends to bring its non-native substrate in the same conformation as its native substrate
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
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
the enzyme physiologically catalyzes the elimination of the enolpyruvyl side chain from isochorismate to make salicylate for incorporation into the siderophore pyochelin
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
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
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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
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
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
loss of the physiological isochorismate synthase catalytic efficiency by three orders of magnitude, and a 2fold gain in isochorismate-pyruvate lyase catalytic efficiency
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
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
the enzyme develops a pH dependence corresponding to a loss of catalytic power upon deprotonation of the histidine. With loss of the positive charge on the K42H side chain at high pH, the enzyme retains lyase activity at about 100fold lowered catalytic efficiency but loses detectable chorismate mutase activity
site-directed mutagenesis of the catalytic residue, the mutant enzyme shows 100fold lowered isochorismate lyase catalytic efficiency compared to the wild-type, but loses detectable mutase activity. It develops a pH-dependence corresponding to a loss of catalytic power upon deprotonation of the histidine. The change is not due to changes in active site architecture, but due to the difference in charge at this key site
mutation leads to the recovery in catalytic free energy of activation of 2.52.7 kcal/mol compared to mutant K42C. Exogenous addition of ethylamine to the K42A variant leads to a neglible recovery of activity, whereas addition of propylamine causes an additional modest loss in catalytic power
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
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
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
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
Structure-function analyses of isochorismate-pyruvate lyase from Pseudomonas aeruginosa suggest differing catalytic mechanisms for the two pericyclic reactions of this bifunctional enzyme
Salicylate biosynthesis in Pseudomonas aeruginosa. Purification and characterization of PchB, a novel bifunctional enzyme displaying isochorismate pyruvate-lyase and chorismate mutase activities
pH Dependence of catalysis by Pseudomonas aeruginosa isochorismate-pyruvate lyase: implications for transition state stabilization and the role of lysine 42
Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB