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You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Function of your protein
Inositol Polyphosphate 1-Phosphatase, gene- INPP1. This enzyme is found in the organism Bos Taurus (Bovine), This enzyme functions specifically in removing a phosphate group from substate inositol. The substrate is IP3 and the product is IP2 (The phosphate got removed). Besides that, this also functions in regulating gluconeogenesis, and sulfur assimilation. The PDB identifier of my focus is 7KIR it contains 1 ligand, and the ligand it shows is (INPP1D54A). The function of is dephosphorylating inositol.
Biological relevance and broader implications
This study is important since the enzyme was not only present in Bos Taurus, but it also presents in different organisms, such as mice and humans, and because of that, it this enzyme should work in the same or very similar ways without change in function. This enzyme helped us have a better understanding of the dephosphorylation of IP3. In addition, IP3 signals are involved in inositol signaling, and cellular communication network, so understanding what ions are important in the activation and inhibition of the inositol signaling are relevant because we could figure out how to stop the IP3 signal and with that it allows us to take control over the metabolic pathways and cellular communication networks. Besides that, this enzyme also functions in regulating gluconeogenesis, and sulfur assimilation, which are the pathways that help a lot in organism function. Therefore, understanding this enzyme is guiding us to a larger understanding of metabolic pathways and molecular of how it works in our body pathways.
Important amino acids
Inositol (1,4)-bisphosphate is a substrate that binds in the active site of INPP1D54A. The phosphate in the substrate serves as a ligand for both the calcium ions- CA1 and CA2.; Glutamic acid (290), Lysine (294), Serine (157), Threonine (158), Glutamic acid (269), and Alanine (291) largely contributed an extensive role in interactions between 1-PO4 and 4-PO4 of the INPP1D54A to the active site. [3]
Threonine is Amphipathic, which means it has both hydrophilic and hydrophobic parts. Serine, Threonine, and Lysine are Polar. Polar hydrophilic amino acids are important in ligand binding to the substrate because it makes the binding site precisely positioned for hydrogen bonding to the hydroxy and carboxylate groups of the substrate. Or in a different way, The charges have become important for locating or identifying the accessible area that helped the protein function. For instance, in this article, the motif of enzymes in this family is DPIDxT, (x can be anything) but in this case, the D54, E80, E79, D153, D317, and T158. These amino acids have negative charges and they hold on the metal ions, which are positive charges, then the metals hold on to the water and substrates. The protein would not function without this holding process. In this study, catalytic amino acid Thr 158 is an outstanding amino acid because it is activated for inline attack the water molecule, and on 1-PO4, which causes the breaking of the bond and forming a new bond in a reaction, also resulting in a phosphate leaving group. [4]
I also found that the Inotisol rings on the end have a lot to do with binding. for binding are Thr 312, Lys 270, Ala 291, Asp 156. These key amino acids are important because they participate in hydrogen bonds, hydrophobic, and ionic bonds.
of the active site with all the important amino acids
[5].
Structural highlights
The contains 77% alpha-helices, 23% beta-sheets. More specific are 13 secondary structural elements of which 10 𝜶-helices and 3 𝛃- strands, 𝜶-helices contain catalytic amino acids and allow all amino acids to form hydrogen bonds with each other. On other hand, 𝛃-sheet does twist to allow better fits in the enzyme. As I observed, there are two large anti-parallel 𝛃-sheet, and with 𝜶-helices, together they help define the structure and function of this protein. There are no quaternary structures in the protein, but this protein does fold in the. As it showing there are hydrophobic, polar interactions hydrogen bonds, an ionic bond, and that form this structure.
models of amino acids here binding to the INPP1D54 show a model of a 3D arrangement in which atoms are partial spheres and the information about composition, the transparency has given the idea that the red substrate is deep in the middle, which lets us know the location of the substrate is in the active site. It also presented how much space an atom occupies, in this protein, the atoms take lots of space, and bond distances are really small between each other. Compared to cartoon visualization it is much easy to understand the basic structure of the atoms than space-filling because space-filling does not provide anything like a realistic sense of molecular size or structure.
Other important features
In structure determination INPP1D54A metal and substates complexes. D54 occurs and results in mutation, which causes Arapratic acid 54 to change to Alaine 54 (). However, even though mutation D54 occurs, but only results in loss of INNPP1 activity, although there is no significant change in substate affinity, likewise it is hypothesized that D54 can be utilized to trap the substate in INPP1. [6]
Magnesium and Lithium are two important in this study, but Li+ is an uncompetitive pattern of inhibition and so as putting Mg and Li in comparison Li could not compete Mg or replace Mg position.
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