User:Cameron Evans/Sandbox 1: Difference between revisions
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===General Structure=== | ===General Structure=== | ||
Prokaryotic glutamate dehydrogenase (GDH) does not have any common quaternary structure among | Prokaryotic glutamate dehydrogenase (GDH) does not have any common quaternary structure among prokaryotes (1EUZ is a hexamer, 1HRD a trimer); however, every prokaryotic structure so far elucidated shows a common overall tertiary structure. | ||
Each monomer (reguardless of quaternary structure) has two domains: | Each monomer (reguardless of quaternary structure) has two domains, each of which have a <scene name='User:Cameron_Evans/Sandbox_1/Secondary/2'> similar overall form</scene>. Both domains are beta sheets flanked by alpha helices. | ||
One domain is a variant of the Rossmann dinucleotide binding fold (<scene name='User:Cameron_Evans/Sandbox_1/Domain_ii/2'>Domain II</scene>) and is involved in cofactor binding; while the other domain is involved in oligomerization (<scene name='User:Cameron_Evans/Sandbox_1/Domain_i/2'>Domain I</scene>). Furthermore, Domain I contains most of the substrate binding residues (discussed below). <ref name="1bgv" /> | |||
===Specificity=== | ===Specificity=== | ||
<scene name='User:Cameron_Evans/Sandbox_1/1bgv_spec_pocket/2'> | <scene name='User:Cameron_Evans/Sandbox_1/1bgv_spec_pocket/2'>Specific interactions of ''Clostridium symbiosum'' GluDH to Glu</scene> are made up of polar interactions from K89 and S380 (to the gamma carbonyl) and hydrophobic interactions from G90, V377 and A163 to the sidechain. The last three residues that make this interaction are highly conserved among amino acid dehydrogenases. <ref name="1bgv" /> | ||
Cofactor? | |||
===Movement=== | |||
<applet load='Temp.pdb' size='200' frame='true' align='right' scene='User:Cameron_Evans/Sandbox_1/Morph_side_view/1' target='0' /> | |||
... | Upon substrate binding, GluDH undergoes an induced change that begins the necessary reaction. This change involves the movement of Domain II some 14 degrees relative to Domain I (which is fixed in the oligomer). This appears to "close" the cleft in which the substrate and the cofactor are bound. To fully terminate the reaction, the movement of the domains in the opposite direction (i.e., to the "open conformation") is required and the products are released. | ||
.. | On the right is an approximation of this movement from available crystal structures. Domain II is highlighted in Blue and Domain I in Purple.(<scene name='User:Cameron_Evans/Sandbox_1/Morph_side_view/2'>Side View</scene>)(<scene name='User:Cameron_Evans/Sandbox_1/Morph_side_view/1'>Top View</scene>) | ||
==Eukaryote== | ==Eukaryote== | ||