Beta-glucosidase: Difference between revisions

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2VRJ is a β-glucosidase which EC number is 3.2.1.21. It comes from ''Thermotoga maritima'' which is a rod-shaped bacterium belonging to the order of Thermotogates. This bacterium was originally isolated from geothermal heated marine sediments. β-glucosidase is in complex with N-octyl-5-deoxy66-oxa-N-carbamoylcalystegine.

In terms of structure 2VRJ is a homodimer. It means that it is composed of two chains <scene name='Sandbox_155/Chain_b/1'>A</scene>and <scene name='Sandbox_155/Chain_a/1'>B</scene> which are chiral. 438 residues are involved in each chain and constitutes a subunit of the protein. Each subunit contains a''' catalytic site'''.

In terms of structure 2VRJ is a homodimer. It means that it is composed of two chains <scene name='Sandbox_155/Chain_b/1'>A</scene> and <scene name='Sandbox_155/Chain_a/1'>B</scene> which are chiral. 438 residues are involved in each chain and constitutes a subunit of the protein. Each subunit contains a''' catalytic site'''.

β-glucosidase is called β-D-glucoside glucohydrolase or cellobiase too.

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The enzymatic hydrolysis of a glycosidic bond requires two critical residues : a proton donor and a proton acceptor which can also be called a nucleophile/base. Aspartate and glutamate have been found to perform catalysis.

β-glucosidases are exocellulases. It means that they act only on the end of the molecule they have to hydrolyse. It implies that the catalytic site has to be near the surface of the protein so that the residues which compose the catalytic site have to be hydrophilic. Glutamate and asparagin are hydrophilic amino-acids .

2VRJ presents two catalytic sites composed of three residues : two residues of glutamate(<scene name='Sandbox_155/166_and_351/4'>166 and 351</scene>)and one residue of asparagin (<scene name='Sandbox_155/~~166_and_351~~/4'>293</scene>).

2VRJ presents two catalytic sites composed of three residues : two residues of glutamate(<scene name='Sandbox_155/166_and_351/4'>166 and 351</scene>)and one residue of asparagin (<scene name='Sandbox_155/293/2'>293</scene>).

===Hydrolysis of terminal non-reducing residues in β-glucosides===

There are two ways to hydrolyse the terminal non-reducing residues in β-glucosides which implicate the two glutamate residues and a molecule of water. Water which is an amphoter, is here used as a base for the nucleophilic attack on the positively charged anomeric carbon.

The general equation of the chemical reaction is :

~~Here the~~ protein is presented in complex with an inhibitor called <scene name='Sandbox_155/Calystegine/1'>calystegine</scene>.We can see that the two '''<font color='#5CB8D1'>glutamate</font>''' residues involved in the catalytic site are really closed to the ligand. Indeed there are interactions between these residues and calystegine.

The protein is presented in complex with an inhibitor called <scene name='Sandbox_155/Calystegine/1'>calystegine</scene>.We can see that the two '''<font color='#5CB8D1'>glutamate</font>''' residues involved in the catalytic site are really closed to the ligand. Indeed there are interactions between these residues and calystegine.

Beta-glucosidase: Difference between revisions

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@@ Line 5: / Line 5: @@
 VRJ is a β-glucosidase which EC number is 3.2.1.21. It comes from ''Thermotoga maritima'' which is a rod-shaped bacterium belonging to the order of Thermotogates. This bacterium was originally isolated from geothermal heated marine sediments. β-glucosidase is in complex with N-octyl-5-deoxy66-oxa-N-carbamoylcalystegine.
-In terms of structure 2VRJ is a homodimer. It means that it is composed of two chains <scene name='Sandbox_155/Chain_b/1'>A</scene>and <scene name='Sandbox_155/Chain_a/1'>B</scene> which are chiral. 438 residues are involved in each chain and constitutes a subunit of the protein. Each subunit contains a''' catalytic site'''.
+In terms of structure 2VRJ is a homodimer. It means that it is composed of two chains <scene name='Sandbox_155/Chain_b/1'>A</scene> and <scene name='Sandbox_155/Chain_a/1'>B</scene> which are chiral. 438 residues are involved in each chain and constitutes a subunit of the protein. Each subunit contains a''' catalytic site'''.
 β-glucosidase is called β-D-glucoside glucohydrolase or cellobiase too.
@@ Line 19: / Line 19: @@
 The enzymatic hydrolysis of a glycosidic bond requires two critical residues : a proton donor and a proton acceptor which can also be called a nucleophile/base. Aspartate and glutamate have been found to perform catalysis.
 β-glucosidases are exocellulases. It means that they act only on the end of the molecule they have to hydrolyse. It implies that the catalytic site has to be near the surface of the protein so that the residues which compose the catalytic site have to be hydrophilic. Glutamate and asparagin are hydrophilic amino-acids .
-VRJ presents two catalytic sites composed of three residues : two residues of glutamate(<scene name='Sandbox_155/166_and_351/4'>166 and 351</scene>)and one residue of asparagin (<scene name='Sandbox_155/166_and_351/4'>293</scene>).
+VRJ presents two catalytic sites composed of three residues : two residues of glutamate(<scene name='Sandbox_155/166_and_351/4'>166 and 351</scene>)and one residue of asparagin (<scene name='Sandbox_155/293/2'>293</scene>).
+===Hydrolysis of terminal non-reducing residues in β-glucosides===
+There are two ways to hydrolyse the terminal non-reducing residues in β-glucosides which implicate the two glutamate residues and a molecule of water. Water which is an amphoter, is here used as a base for the nucleophilic attack on the positively charged anomeric carbon.
+The general equation of the chemical reaction is :
-Here the protein is presented in complex with an inhibitor called <scene name='Sandbox_155/Calystegine/1'>calystegine</scene>.We can see that the two '''<font color='#5CB8D1'>glutamate</font>''' residues involved in the catalytic site  are really closed to the ligand. Indeed there are interactions between these residues and calystegine.
+The protein is presented in complex with an inhibitor called <scene name='Sandbox_155/Calystegine/1'>calystegine</scene>.We can see that the two '''<font color='#5CB8D1'>glutamate</font>''' residues involved in the catalytic site  are really closed to the ligand. Indeed there are interactions between these residues and calystegine.