Wenqi Yan 994939766 Chem124A Extradiol Oxygenase Introduction: In general, Oxygenase is any enzyme that transfers oxygen atom from O2 to oxidize other compounds. There are two types of oxygenase: Monooxygenase and Dioxygenase. Monooxygenase transfers one oxygen atom from the O2 to the compound and reduce the other oxygen atom in O2. In dioxygenase, both oxygen atoms are transfer to the compound. For this essay, the type of oxygenase will be cover to demonstrate the extradiol oxygenase is Dioxygenase. There are two types of Dioxygenase: Intradiol and Extradiol Dioxygenase. The type of dioxygenase enzyme will be using in this essay is Catechol 1, 2-dioxygenase and Catechol 2, 3-dioxygenase. They are metalloprotein enzymes that cleave the bond at ortho- or meta- position to the two hydroxyl groups in catechol by oxidizing the two hydroxyl groups into carboxylic acid (Lindsay). Figure 1 below illustrate an example of a reaction that catalyzed by catechol 1, 2-dioxygenase for an intradiol dioxygenase. Figure 1: Reaction of intradiol dioxygenase (Wikipedia.org) However, this essay will be focusing on the extradiol dioxygenase: Catechol 2, 3-dioxygenase. Figure2 below is the illustration of such reaction. It is called extradiol 2, 3-dioxygenase because it adds the oxygen atoms to the 2 and 3 position which makes the product to have an extra hydroxyl group than the reactant. Figure2: Reaction of extradiol dioxygenase (Aaron 2004) The Catechol 2, 3-dioxygenase is encoded by the receptor called Pseudomonas putida. It is an organism that capable of converting styene oil into the biodegradable plastic (Ward). Structure: The structure of Catechol 2, 3-dioxygenase is shown in figure3. The iron (II) metal center in the catechol 2, 3-dioxygenase is bonded to two hisidine moieties, one glutamate moiety and two water molecules in a square pyramidal structure (Aaron 2004). The difference in the oxidation state of the center Fe metal determines what product to from. For instance, if the center metal is Fe (III) instead of Fe (II), the reaction will form the product of intradiol dioxygenase rather than the extradiol dioxygenase (Aaron 2004). Figure4 below shows the three-dimensional structure of extradiol dioxygenase when it bind to its receptor Pseudomonas putida (PDB). The PDB code for the cystal structure of catechol 2, 3-dioxygenase is 3HPV. Figure 3: Extradiol Dioxygenase (Aaron) Figure 4: Crystal Structure of extradiol 2, 3-dioxygenase (PDB data bank) Symmetry amd Spectrometry: According to the information provided by the Protein Data Bank, the x-ray diffraction showed that Catechol 2, 3-dioxygenase has an orthorhombic structure because all the angle in the unit cells are equal to 90 and the three side length are not equal (PDB). The three side length for Catechol 2, 3-dioxygenase are a=94.90Å, b=97.00Å and c=133.40Å (PDB). Catechol 2, 3-dioxygenase is a non-linear molecule. It does not have tetrahedral, icosahedral or octahedral symmetry because it has a square pyramidal structure. There is no principle Cn axis, mirror plane nor centre of inversion because the attachments on the center Fe (II) metal are three different types of chemical groups. Therefore it is C1 point group molecule. There are no measurements found for IR and Raman spectroscopy for Catechol 2, 3-dioxygenase. So the IR and Raman activities for this enzyme are not known. Reaction and Mechanism: The extadiol 2, 3-dioxygenase (Catechol 2, 3-dioxygenase) catalyzes the reaction by attaching the center Fe (II) metal to the two oxygen atoms on the benzene ring to replace the two water molecules. Then the O2 will make a direct linkage to the center Fe (II) metal. The oxygen on the other end of the O2 will make a linkage to the position 2 carbon on the benzene ring. Then the linkage between the O2 and Fe (II) metal will break. The oxygen will attach to the position 2 carbon on the benzene ring to form a seven member ring. With the addition of the two water molecules attaching back to the center Fe (II) metal, the linkage between the center Fe (II) metal and the oxygen will break and the oxygen in the seven member ring will be cleaved to form the product and regenerate the catalyst extradiol dioxygenase. Figure 5 below illustrate the catalytic cycle for this extradiol dioxygenase. Figure 5: Mechanism of extradiol dioxygenase (EARCD) Conclusion: In conclusion, extradiol 2, 3-dioxygenase enzymes break the carbon-carbon bond between the two alcohol groups in catechol. Then the position 2 carbon will change from an alcohol group into a carboxylic acid and the addition of OH group to the position 3 carbon. Reference: 1. Aaron K. Justice “Catechol Dioxygenases: Structure and Mechanism” October 19, 2004. 2. “Extradiol aromaticring cleavage dioxygenases (EARCD)” February 1, 1999. http://metallo.scripps.edu/PROMISE/EARCD.html 3. Lindsay D. Eltis and Jeffrey T Bolin. “Evolutionary Relationships among Extradiol Dioxygenases”. May 20, 1996. 4. Protein Data Bank (PDB). “Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28”. May 24, 2010. 5. Ward PG, Goff M, Donner M, Kaminsky W, O'Connor KE. (2006) A two step chemo-biotechnological conversion of polystyrene to a biodegradable thermoplastic. Environmental Science and Technology 40(7):2433-7.
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