| Tryptophan synthase is composed of both alpha helixes and beta sheets. These structures are arranged in a alpha/beta barrel. Specifically, they are arranged in a TIM barrel with eight parallel strands of beta sheets that have eight parallel alpha helixes connecting them.
The active site of the enzyme can be found just inside the barrel structure. Asp60 and Glu49 are key in binding the indol-3-glycerol-phosphate when it enters the barrel.
It is here that Asp60 will cause the cleavage of the carbon-carbon bond and will eventually cause the formation of a double bonded oxygen. |
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| Pectate lyase is composed primarily of beta sheets. These sheets are arranged in a parallel fashion with each sheet connecting to the next sheet so it resembles a cork screw.
The active site is found on strands 3,4, and 6. Strands 3 and 4 contribute Asp137, Asp136, and Asp 200, while strand 6 has a key arginine at Arg223. All of these amino acids face the outside of the enzyme.
The arginine will supply a temporary bond plaseholder while the beta-elimination mechanism takes place and cleaves the pectate. This is not shown because this structure has yet to be solved for when bound to pectate |
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| Aputinic/apyrimidinic endonuclease is composed of both beta sheets and alpha helixes. These combine to form a topology classified as Deoxyribonuclease I. the beta sheets are concentrated on the interior of the enzyme and are a mixture of parallel and anti-parallel.
The active site is found on the side of the enzyme. His309, Asp210, and Asn212 are the key amino acids in binding the substrate.
The Asn212 residue can complement the charge on the phosphate that is to the 5' end of the mismatched base in the DNA strand. This along with the help of Asp 210 will cause a break in the oxygen bond to the phosphate and cause the phosphate to form a double bond with a different oxygen that was previously a single bond. |
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