Sandbox Reserved 819: Difference between revisions
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<StructureSection load='2z55' size='300' side='right' caption='2z55: cristal made of four Archaerhodopsin-2' scene=''> | <StructureSection load='2z55' size='300' side='right' caption='2z55: cristal made of four Archaerhodopsin-2' scene=''> | ||
=2Z55= | |||
__TOC__ | |||
==Introduction== | ==Introduction== | ||
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The 2,3-di-phytanyl-glycerol [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/L2P] (C43 H88 O3) is an archaeol (di-O-phytanylglycerol). This is a double ether of sn-1-glycerol where positions 2 and 3 are bound to phytanyl residues. The archaeols are Archaea homologs of diacylglycerols (DAGs). | The 2,3-di-phytanyl-glycerol [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/L2P] (C43 H88 O3) is an archaeol (di-O-phytanylglycerol). This is a double ether of sn-1-glycerol where positions 2 and 3 are bound to phytanyl residues. The archaeols are Archaea homologs of diacylglycerols (DAGs). | ||
It interacts with the aR2 surface and the carbohydrate <scene name='56/568017/Glc/1'>GLC</scene>. It binds to: the A chain thanks to a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks to a hydrogen bond with the <scene name='56/568017/ | It interacts with the aR2 surface and the carbohydrate <scene name='56/568017/Glc/1'>GLC</scene>. It binds to: the A chain thanks to a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks to a hydrogen bond with the <scene name='56/568017/Tyr85/1'>Tyrosine 85</scene>; the B chain thanks to a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks to a hydrogen bond with the Tyrosine 85; the D chain thanks to a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks to a hydrogen bond with the Tyrosine 85; the E chain thanks to a covalent bond with the carbohydrate alpha-D-glucose 284 (GLC) and thanks to a hydrogen bond with the Tyrosine 85. Others bonds exist like van-der-waals bonds [http://www.ebi.ac.uk/pdbe-site/pdbemotif/?tab=boundmolecule&pdb=2z55&ligandCode3letter=L2P]. | ||
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56% of the Archaeorhodopsin-2 sequence is identical to the [[Bacteriorhodopsin]] sequence.<ref name="seq">PMID: 1654776</ref> | 56% of the Archaeorhodopsin-2 sequence is identical to the [[Bacteriorhodopsin]] sequence.<ref name="seq">PMID: 1654776</ref> | ||
Most amino acids that play a role in the trimerization are not conserved between the two proteins. For instance, the counterparts of some hydrophobic residues of the Archaerhodopsin-2 (the one interacting with the polyene chain of the bacterioruberin) have a different volume. Another difference is the fact that the | Most amino acids that play a role in the trimerization are not conserved between the two proteins. For instance, the counterparts of some hydrophobic residues of the Archaerhodopsin-2 (the one interacting with the polyene chain of the bacterioruberin) have a different volume. Another difference is the fact that the polar residues of the Archaerhodopsin-2 (responsible for the hydrogen bonds with the bacterioruberin) are replaced in the Bacteriorhodopsin by hydrophobic amino acids. | ||
However the global structures of Archaeorhodopsin-2 and | However the global structures of Archaeorhodopsin-2 and Bacteriorhodopsin are really similar, especially at the level of the open space between the monomers. The interaction between the monomers of the Bacteriorhodopsin is also mediated by lipids: diphytanyl diether phospholipids instead of Bacterioruberin. | ||
This similarity of structure forms the basis of several hypothesis concerning the mechanisms of the Archaeorhodopsin-2 <ref name="multiple">PMID:18082767</ref> | This similarity of structure forms the basis of several hypothesis concerning the mechanisms of the Archaeorhodopsin-2 <ref name="multiple">PMID:18082767</ref> | ||
