Group:SMART:2010 Pingry SMART Team: Difference between revisions

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<applet load='1LWI_chainA.pdb' size='400' frame='true' align='left' caption='1lwi, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with NADP+ cofactor' scene='2010_Pingry_SMART_Team/1lwi_default/7'/>
<applet load='1LWI_chainA.pdb' size='400' frame='true' align='left' caption='1lwi, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with NADP+ cofactor' scene='2010_Pingry_SMART_Team/1lwi_default/7'/>
====PDB ID: 1lwi, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with NADP+ cofactor====
====PDB ID: 1lwi, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with NADP+ cofactor====
 
Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase is abbreviated 3α-HSD.
Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase is often abbreviated to 3α-HSD.
Both NADPH (cofactor) and Testosterone (substrate, not shown) are colored CPK. NADPH can be distinguished by its orange phosphorus atoms.
 
Both NADPH (cofactor) and Testosterone (substrate) are colored CPK. NADPH can be distinguished by its orange phosphorus atoms.
 
 
<scene name='2010_Pingry_SMART_Team/1lwi_default/5'>Non-polar cavity for substrate binding is colored CPK. Leu54, Tyr55, Trp86, Phe118, Phe129, and Tyr216 are hydrophobic amino acids found in the pocket.</scene> The reason why the substrate binding pocket is non-polar is that the substrate, testosterone, is a lipid and therefore hydrophobic. This is an important factor when considering how to modify substrate specificity. In Dr. Banta's fuel cell protein, the most common substrate will probably be some type of sugar, which is a hydrophilic molecule. Therefore, the substrate binding pocket must match the substrate. The catalytic triad, which includes the most important amino acids in regards to reacting with the substrate is at the distal, or far, end of the pocket.
 


<scene name='2010_Pingry_SMART_Team/1lwi_cofactorbonding/1'>Orange highlights the co-factor specificity side-chains.</scene> Gln190, Asn167, Ser166 form hydrogen bonds with the nicotinamide ring. For more details about co-factor specificity, see the other two protein structures.
<scene name='2010_Pingry_SMART_Team/1lwi_default/5'>The non-polar cavity for substrate binding is colored CPK. Leu54, Tyr55, Trp86, Phe118, Phe129, and Tyr216 are hydrophobic amino acids found in the pocket.</scene> The substrate binding pocket is non-polar because the substrate, testosterone, is a lipid and therefore hydrophobic. This is an important factor when considering how to modify substrate specificity. In Dr. Banta's fuel cell protein, the most common substrate will probably be a sugar, a hydrophilic molecule. In this case, the substrate binding pocket would be polar.  


The catalytic triad, which includes the most important amino acids in regards catalysis, is located at the far end of the pocket.


<scene name='2010_Pingry_SMART_Team/1lwi_catalytic_triad/1'>Cyan highlights the catalytic triad: Tyr55, Asp50, and Lys84.</scene> These three amino acids perform a reaction called a proton relay to transfer electrons between substrate and cofactor. 3α-HSD is capable of running the reaction both ways, either oxidizing or reducing the substrate and cofactor depending on the state in which testosterone must be. Tyr55 acts as acid, donates proton to steroid-->Tyr55 forms hydrogen bond to Lys84 to stabilize-->Lys84 forms salt link to Asp50 for further stability. In Dr. Banta's protein, this reaction must only be run so that the sugar will be oxidized to reduce the cofactor. The transfer of electrons from cofactor to circuit is already fairly efficient, but the key to an efficient reaction is in transfering the electron from substrate to cofactor. This is where the catalytic triad is extremely important.
<scene name='2010_Pingry_SMART_Team/1lwi_cofactorbonding/1'>Orange highlights the co-factor specificity side-chains.</scene> Gln190, Asn167, Ser166 form hydrogen bonds with the nicotinamide ring in the cofactor. For more details about co-factor specificity, see the other two protein structures, which explain the subject in more depth.


<scene name='2010_Pingry_SMART_Team/1lwi_catalytic_triad/1'>Cyan highlights the catalytic triad: Tyr55, Asp50, and Lys84.</scene> These three amino acids perform a proton relay reaction to transfer electrons between substrate and cofactor. 3α-HSD is capable of running the reaction both ways, either oxidizing or reducing the substrate and cofactor depending on the state of the testosterone. Tyr55 acts as acid, and donates a proton to the steroid-->Tyr55 forms a hydrogen bond to Lys84 for stabilization-->Lys84 forms a salt link to Asp50 for further stability.
In Dr. Banta's protein, this reaction must only be run so that the sugar will be oxidized and the cofactor, reduced. The transfer of electrons from cofactor to circuit is already fairly efficient, but the key to an efficient reaction is in transferring the electron from substrate to cofactor. This is where the catalytic triad is extremely important.


Dark Grey highlights the beta barrel and helix structure. The barrel consists of eight parallel beta strands and eight anti-parallel alpha helices. The bottom is sealed by two antiparallel beta strands (6-10 and 13-18). This structure is common to all members of the AKR family. It provides a convenient way to keep all reactants in the same vicinity and out of the external environment. This applies to reactions in both 3α-HSD and in alcohol dehydrogenase. <scene name='2010_Pingry_SMART_Team/1lwi_betabarrel/4'>Click Here to view the Beta barrel in blue and Helices in red.</scene> The top contains two solvent exposed loops (loop A: 116-142 and loop B: 217-235)
Dark Grey highlights the beta barrel and helix structure. The barrel consists of eight parallel beta strands and eight anti-parallel alpha helices. The bottom is sealed by two antiparallel beta strands (6-10 and 13-18). This structure is common to all members of the AKR family. It provides a convenient way to keep all reactants in the same vicinity and out of the external environment. This applies to reactions in both 3α-HSD and in alcohol dehydrogenase. <scene name='2010_Pingry_SMART_Team/1lwi_betabarrel/4'>Click Here to view the Beta barrel in blue and Helices in red.</scene> The top contains two solvent exposed loops (loop A: 116-142 and loop B: 217-235)


 
<scene name='2010_Pingry_SMART_Team/1lwi_loops/1'>Purple and Blue highlight the two solvent exposed loops (Purple: Loop A, Blue: Loop B)</scene>. The loops are important for two reasons. Loop A is responsible for substrate binding. It contains many of the amino acids that create the hydrophobic substrate binding pocket. Loop B is also important to substrate binding, as it undergoes a large conformational change to accommodate the substrate. In this structure (1lwi), the substrate is absent and this loop is in its extended position. Since this loop in its extended position is in motion, an exact location can not be specified. Hence, residues Ser221 to Lys225 appear to be "missing" even though they are present in the actual protein. This opening and closing "garage door" mechanism is convenient for working through a large number of substrates, as the substrates can enter and exit easily. In the rat liver, each protein needs to convert as many steroids as possible to change the signal that is being sent out. In Dr. Banta's fuel cell, each protein would need to oxidize sugar molecules quickly to establish a current.
<scene name='2010_Pingry_SMART_Team/1lwi_loops/1'>Purple and Blue highlight the two solvent exposed loops (Purple: Loop A, Blue: Loop B)</scene>. The loops are important for two different reasons. Loop A is responsible for the substrate binding. It holds many of the amino acids responsible for the hydrophobic substrate binding pocket. Loop B is also important to substrate binding, as it undergoes large conformational changes to accommodate the substrate. In this structure (1lwi), the substrate is absent and this loop is in its extended position. Furthermore, since this loop in its extended position is in motion, we cannot specify an exact location. Hence, residues Ser221 to Lys225 appear to be "missing" even though they are present in the actual protein. This opening and closing "garage door" mechanism is convenient for working through a large number of substrates, as the substrates can enter and exit easily. In the rat liver, each protein needs to convert as many steroids as possible to change the signal that is being sent out. In Dr. Banta's fuel cell, each protein would need to oxidize sugar molecules quickly to establish a current.
 
<scene name='2010_Pingry_SMART_Team/1lwi_default/7'>Revert to default scene display</scene>
<scene name='2010_Pingry_SMART_Team/1lwi_default/7'>Revert to default scene display</scene>
 
 
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<applet load='1AFS_chainA.pdb' size='400' frame='true' align='left' caption='1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone' scene='2010_Pingry_SMART_Team/1afs_default/7'/>
<applet load='1AFS_chainA.pdb' size='400' frame='true' align='left' caption='1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone' scene='2010_Pingry_SMART_Team/1afs_default/7'/>


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