Beta-glucosidase: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
|||
| Line 4: | Line 4: | ||
=== Origin and global structure of 2VRJ=== | === Origin and global structure of 2VRJ=== | ||
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. | 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 [1]. | ||
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. Each chain is composed of 438 residues 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. Each chain is composed of 438 residues and constitutes a subunit of the protein. Each subunit contains a''' catalytic site'''. | ||
===Biocatalyst=== | ===Biocatalyst=== | ||
A β-glucosidase is an '''enzyme''' which catalyses the hydrolysis of terminal non-reducing residues in β-glucosides. It acts on the '''β(1-4) bond linking''' two glucose residues or glucose-substituted molecules. The action of the enzyme on such glucosides results in the release of units of glucose. For instance, hydrolysis of cellobiose catalysed by a β-glucosidase releases two glucoses. | A β-glucosidase is an '''enzyme''' which catalyses the hydrolysis of terminal non-reducing residues in β-glucosides. It acts on the '''β(1-4) bond linking''' two glucose residues or glucose-substituted molecules. The action of the enzyme on such glucosides results in the release of units of glucose. For instance, hydrolysis of cellobiose catalysed by a β-glucosidase releases two glucoses [2]. | ||
[[ Image:Cellobiose.jpg]][[Image:Suite.jpg]] | [[ Image:Cellobiose.jpg]][[Image:Suite.jpg]] | ||
| Line 19: | Line 19: | ||
===Structure and function=== | ===Structure and function=== | ||
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 [ | 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 [3]. Accorded to this, studies showed that one of the conserved regions of β-glucosidases is centred on conserved glutamate residues [4]. | ||
As every β-glucosidase, 2VRJ presents two conserved residues of glutamate (<scene name='Sandbox_155/166_and_351/4'>166 and 351</scene>). Moreover 2VRJ has a third important residue : <scene name='Sandbox_155/293/2'>asparagin 293</scene>. | As every β-glucosidase, 2VRJ presents two conserved residues of glutamate (<scene name='Sandbox_155/166_and_351/4'>166 and 351</scene>). Moreover 2VRJ has a third important residue : <scene name='Sandbox_155/293/2'>asparagin 293</scene> [5]. | ||
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 and the asparagin are really closed to each other and to the ligand (<scene name='Sandbox_155/Ligand_and_residues/1'>see</scene>). Such a proximity highly suggests that there are important interactions between them. So we can say that the catalytic site of 2VRJ is composed of two glutamate and one asparagin. | 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 and the asparagin are really closed to each other and to the ligand (<scene name='Sandbox_155/Ligand_and_residues/1'>see</scene>). Such a proximity highly suggests that there are important interactions between them. So we can say that the catalytic site of 2VRJ is composed of two glutamate and one asparagin. | ||
There are three different topologies for the active site of β-glucosidases : the pocket or crater, the cleft or groove and the tunnel [ | There are three different topologies for the active site of β-glucosidases : the pocket or crater, the cleft or groove and the tunnel [3]. The topology of 2VRJ active site is a <scene name='Sandbox_155/Pocket/1'>pocket</scene> in which the ligand can bind. | ||
===Hydrolysis of terminal non-reducing residues in β-glucosides=== | ===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. | 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 [6]. 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 : | The general equation of the chemical reaction is : | ||
| Line 57: | Line 57: | ||
== References == | == References == | ||
[1] Aguilar M, Gloster T M, García-Moreno I M, Ortiz Mellet C, Davies G J, Llebaria A, Casas J, Egido-Gabás M, García Fernandez J M. Molecular Basis for β-Glucosidase Inhibition by Ring-Modified Calystegine Analogues. ChemBioChem 2008 ; 9 (16) : 2612-8. | |||
http:// | [2] http://en.wikipedia.org/wiki/B-glucosidase | ||
http:// | [3] Davies G, Henrissat B. Structures and mechanisms of glycosyl hydrolases. Structure 2004 ; 3 (9) : 853-9. | ||
[4] http://www.ebi.ac.uk/interpro/IEntry?ac=IPR018120#PUB00002205 | |||
[5] http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/CSA/CSA_Site_Wrapper.pl?pdb=2vrj | |||
[6] http://www.cazy.org/fam/ghf_INV_RET.html#3 | |||
(http://www.ebi.ac.uk/pdbe-srv/view/entry/2vrj/viewer) ? | |||
