Prp40: Difference between revisions

[[Image:Prp40 domains.PNG|500px|thumb|left|upright=4|alt=Proposed domains.|Schematic representation of the domain organization in Prp40.]]   

The <scene name='Sandbox_504/Start_scene/1'>overall structure of the two consecutive WW domains</scene> follows that of one triple curved antiparallel β-strand sheet connected to the other by an α-helical linker composed of residues <scene name='Sandbox_504/Linker/1'>Lys30-Glu42</scene>. The residues in each of the β strands are as follows, β1 <scene name='Sandbox_504/Wwdomain1_b1/2'>(Trp4-Asp9)</scene>, β2 <scene name='Sandbox_504/Wwdomain1_b2/1'>(Arg13-Thr19)</scene>, and β3 <scene name='Sandbox_504/Wwdomain1_b3/1'>(Lys22-Trp26)</scene> in the <scene name='Sandbox_504/Ww1/2'>first W domain</scene>, and β1 <scene name='Sandbox_504/B1_of_ww2/1'>(Trp45-Thr50)</scene>, β2 <scene name='Sandbox_504/B2_of_ww2/1'>(Lys54-Pro60)</scene>, and β3 <scene name='Sandbox_504/B3_of_ww2/1'>(Arg63-Trp67)</scene> in the <scene name='Sandbox_504/Ww2/1'>second W domain</scene>.  Located on the convex surface of each of the domains lie three residues, <scene name='Sandbox_504/Hydrophobicresiduesandprotein/1'>Trp4/45, Tyr16/57, and Pro29/Leu40</scene>, that form a <scene name='Sandbox_504/Hydrophobicresiduesandprotein/2'>hydrophobic core</scene>.  On the concave surface lies an aromatic pocket comprised of the residues <scene name='Sandbox_504/Aromatic_pocket_residues/1'>Tyr15/56, Tyr17/58, and Trp26/67</scene>.  These pockets makes up the ligand binding sites on each of the WW domains, however they do not form one large pocket, rather <scene name='Sandbox_504/Aromatic_pocket_residues/2'>two separate small pockets </scene> that face away from each other.  The linker residues Leu32 and Leu40 fold back into the hydrophobic cores of the WW domains<ref name ="wiesner"/>.  

The <scene name='Sandbox_504/Start_scene_ff1/1'>FF1 domain of Prp40 is comprised of three alpha helices</scene>, and one 310 helix located between α2 and α3.  Helices are composed of the following residues, <scene name='Sandbox_504/Ff1_a1/1'>α1</scene> (134-146), <scene name='Sandbox_504/Ff1_a2/2'>α2</scene> (154-163), <scene name='Sandbox_504/Ff1_310/1'>310</scene> (167-170), and <scene name='Sandbox_504/Ff1_a3/1'>α3</scene> (175-187).  The core domain is made up of a series of aromatic and aliphatic residues.  A type 1 β-turn is exhibited by the residues Asp149, Ser150, Thr151, and Trp152<ref name ="gasch"/>.

<scene name='Sandbox_504/Start_scene_ff4/1'>Domain FF4 of Prp40</scene> exhibits compact four helical bundle fold comprised of an α1-α2-310-α3 topology.  The composition of each helix is a follows <scene name='Sandbox_504/A1_of_ff4/1'>α1</scene> (Glu489-Thr507), <scene name='Sandbox_504/A2_of_ff4/1'>α2</scene> (Trp519-Leu526), <scene name='Sandbox_504/310_of_ff4/1'>310</scene> (Tyr532-Gly536) and <scene name='Sandbox_504/A3_of_ff4/1'>α3</scene> (Asp539-Phe549). There are a series of interactions between the different helices, for example Tyr532 is in contact with Phe500, Leu503, Ser523, and Arg542.  A difference between FF1 and FF4 is the presence of five extra amino acids in F4 which gives the <scene name='Sandbox_504/Loop_of_ff4/1'>loop</scene> located between α 1 and α2 an extra turn.  This insertion however does not increase the flexibility of F4 as compared to F1<ref name ="bonet"/>.