Function(s) and Biological Relevance
Secondary structure is important in Bap1. 6MLT is composed of two major domains, the beta-prism domain and the beta-propeller domain. Yellow represents the beta-helix, with pink showing the alpha-helix, white showing coils and loops, and turns in blue.
One of the major functions of Bap1 is it's sugar binding properties. This image shows the binding pocket on the beta-prism, which is where carbohydrates bind. The molecule is shown in spacefill and is colored based on hydrophobicity. Hydrophilic residues are shown in blue, with hydrophobic residues in red, and non charged residues in white. Lys, which makes up a large part of the binding pocket is represented in pink. The positively charged side chain on Lys makes it great for negatively charged sugars to bind to.
Asp 348, which is found on the beta-prism of Bap1, plays a crucial role in binding to citrate and carbohydrates. Mutation of aspartic acid to alanine results in a loss of function for Bap1. Since Ala has a much smaller side chain than Asp, it becomes too many Å away to interact.
There are six essential amino acids involved in the binding of citrate. These six amino acids include Gly 344, Ala 345, Val 346, Lys 501, Asp 348, and His 500. Gly 344, Ala 345, Val 346, Lys 501 all interact with citrate via hydrogen bonding, while Asp 348 and His 500 interact via van der Waals interactions. The amino acids are shown in CPK to highlight properties that correspond with hydrogen bonding.
Broader Implications
Structural highlights and structure-function relationships
Energy Transformation
This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
