2014-01-04T15:45:39Z

Allan Bernard:

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='''2Z55'''=
{{STRUCTURE_2z55| PDB=2z55 | SCENE= }}
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==The trimeric structure of Archaerhodopsin-2==

Archaerhodopsin-2 (aR2) is a light-driven proton pump. The resulting proton gradient is subsequently converted into chemical energy.

Archaerhodopsin-2 is a retinal protein–carotenoid complex found in the claret membrane of Halorubrum sp. aus-2 and it represents a real adaptation to life at high salt concentrations. In these membranes, three Archaerhodopsin-2 or chains form a trimeric structure [http://www.pdb.org/pdb/explore/jmol.do?structureId=2Z55&view=symmetry&bionumber=1], capturing light energy and using it to move protons across the membrane out of the cell. It exists four different chains with different structures: A,B,D,E (they are not represented here).
The trimerization increases the thermal stability of the protein aR2 in the claret membrane of Halorubrum sp. aus-2 and enlarges the pH range where the protein can keep its neutral purple conformation. Thus, a larger pH gradient can be generated across the membrane, leading to an increased efficiency of the proton pumping. Therefore the trimeric structure is more efficient than the monomeric structure.

Archaerhodopsin-2 consists of the protein moiety rhodopsin and a reversibly covalently bound cofactor, the retinal.
The trimeric structure functions as a light-driven proton pump thanks to this retinal molecule, called <scene name='56/568017/New_scene_ret_2/1'>RET</scene>, which changes its conformation when absorbing a photon, resulting in a conformational change of the surrounding protein and the proton pumping action.

Others ligands are linked with each subunit of the trimeric structure like the bacterioruberin (<scene name='56/568017/22b/1'>22B</scene>). THe bacterioruberin plays a structural role for the trimerization of aR2.
Several saccharides are also linked to the trimeric structure.
Some lipids and glycolipids interact with the trimeric structure like the 2,3-di-phytanyl-glycerol (<scene name='56/568017/New_scene_3/1'>L2P</scene>) . They fill the intratrimer hydrophobic space and they are required to the complex activity. Others lipids surround the trimeric structure, which is essential to preserve it.<ref>PMID:18082767</ref>

===The rhodopsin===

The rhodopsin belongs to the CATH Superfamily 1.20.1070.10[http://www.cathdb.info/version/3.5.0/superfamily/1.20.1070.10]

The protein <scene name='56/568017/Rhodopsin/1'>rhodopsin</scene> has 7 transmembrane alpha helices, embedded in the plasma membrane. These helices are connected to each other by protein loops.

The rhodopsin harvests energy from light to carry out metabolic processes using a non-chlorophyll-based pathway. Thanks to the retinal, the light induces a phototactic response by interacting with transducer membrane-embedded proteins that have no relation to G proteins. There are four different rhodopsins with different structures: A, B, D, E.

===Structure and functioning of the Retinal (RET)===

The retinal (C20 H28 O) is a photoreactive chromophore.
The rhodopsin binds retinal [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/RET] in a central pocket on the seventh helix by a covalent bond with the <scene name='56/568017/Lysine_221/1'>lysine residue 221</scene>. Others bonds exist, like van-der-waals bonds [http://www.ebi.ac.uk/pdbe-site/pdbemotif/?tab=boundmolecule&pdb=2z55&ligandCode3letter=RET].

Retinal is a polyene chromophore and allows to convert light into metabolic energy. It absorbs visible light maximally at 550-570 nm.
It catches a photon, leading to a conformational change of the rhodopsin. This is an isomerization of the 11-cis-retinal into a ll-trans-retinal. Retinal binds covalently to the lysine 221 on the transmembrane helix nearest the C-terminus of the protein through a Schiff base linkage. Formation of the Schiff base linkage involves removing the oxygen atom from retinal and two hydrogen atoms from the free amino group of lysine, giving H2O. Retinylidene is the divalent group formed by removing the oxygen atom from retinal, and so opsins is called retinylidene proteins. A Schiff base is a compound with a functional group made up of a carbon-nitrogen double bond with a nitrogen atom connected to an aryl or alkyl group, not hydrogen. Schiff bases in a broad sense have the general formula R1-R2-C=N-R3, where R is an organic side chain. In this definition, Schiff base is synonymous with azomethine. The chain on the nitrogen makes the Schiff base a stable imine. A Schiff base derived from an aniline, where R3 is a phenyl or a substituted phenyl.

==Ligands==

===The bacterioruberin (22B)===

The bacterioruberin [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/22B], C50 H76 O4, is a 50 carbon carotenoid pigment which give a red color to the membrane. The primary role of bacterioruberin in the cell is to protect against DNA damage incurred by UV light. This protection is not, however, due to the ability of bacterioruberin to absorb UV light. Bacterioruberin protects the DNA by acting as an antioxidant, rather than directly blocking UV light. It is able to protect the cell from reactive oxygen species produced from exposure to UV by acting as a target.
Furthermore, the bacterioruberin is essential because it plays a structural role for the trimerization of aR2.
It binds to: the B chain thanks to a hydrogen bond with the <scene name='56/568017/Threonine_112/1'>Threonine 112</scene>, the <scene name='56/568017/Tyrosine/1'>Tyrosine 156</scene> and the HOH 304 thanks to an electrosatic bond; the D chain thanks to a hydrogen bond with the Tyrosine 156; the E chain thanks to a hydrogen bond with the Tyrosine 156.(others bonds exist like van-der-waals bonds [http://www.ebi.ac.uk/pdbe-site/pdbemotif/?tab=boundmolecule&pdb=2z55&ligandCode3letter=22B])

===The 2,3-di-phytanyl-glycerol (L2P)===

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/Tyr_85/1'>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])

===Saccharides===

Several saccharides can interact with the trimeric structure: β-D-galactose [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/GAL], α-D-glucose [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/GLC] and α-D-mannose[http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/MAN].

These saccharides interact with the trimeric structure but also with each other and sometimes with the 2,3-Di-Phytanyl-Glycerol.
Three α-D-glucose are bound to the Archaerhodopsin-2: one for each monomer. Each glucose forms a covalent bond with a molecule of 2,3-Di-Phytanyl-Glycerol and one with a molecule of α-D-mannose.
Three α-D-mannose (one for each monomer) interact with the Archaerhodopsin-2. Each mannose forms two covalent bonds with others saccharides: one with a molecule of α-D-glucose and one with a molecule of β-D-galactose. (A VERIFIER ! 1 OU 2 / GALACTOSE ? 3 OU 6 MANNOSES ?)

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=2z55

== External ressources ==

== References ==
<references />