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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
My protein is found in the Streptomyces coelicolor, but being expressed system in Escherichia coli. The specific function of Chorismate dehydratase is to catalyze the dehydration of chorismate to produce 3-enolpyruvyl-benzoate (3-EPB). Chorismate dehydratase has two ligands, both are (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid (ISJ). The two ISJ molecules are on different of lobes of Chorismate dehydratase (Lobe A and Lobe B).
Biological relevance and broader implications
Not much is known about the futalosine pathway and the way it works. MqnA is the first enzyme of the futalosine pathway catalyzing the dehydration of chorismate to yield 3-enolpyruvyl-benzoate (3-EPB), a reaction not observed for any other enzyme. Chorismate is the product of the shikimate pathway and the precursor of many aromatic compounds including the amino acids in addition to the electron carriers ubiquinone and menaquinone. As enzymes of the shikimate pathway, as well as enzymes that convert chorismate, are only present in bacteria, fungi, and plants, they are promising targets for antimicrobials and herbicides.
Important amino acids
The catalytic amino acids in my enzyme are ALA18, SER87, and TYR243. These three amino acids would be considered the catalytic triad.
ISJ (A) has the following Hydrogen bonds with ScMqnA: THR60, SER87, CYS88, SER110, ARG111, THR112, SER113, GLY152.
ISJ (A) has the following Hydrophobic interaction with ScMqnA: PRO42, VAL79, VAL85, PHE186, TYR243
ISJ (B) has the following Hydrogen bonds with ScMqnA: THR60, SER87, CYS88, SER110, ARG111, THR112, SER113, GLY152, PHE187, THR243
ISJ (B) has the following Hydrophobic interaction with ScMqnA: PRO42, VAL79, VAL85, ILE151, PHE187
Structural highlights
The Secondary structures has 20 beta sheets, 28 alpha helices, and several random coils. The tertiary structure would be described as globular as is it in a shape of a ball, with an alpha clamp and two lobes connected by two linkers. The beta sheets contain all three of the catalytic amino acids and most of the important binding amino acids.
Other Important Features
Chorismate dehydratas uses a Venus flytrap (VFT) fold found typically in ligand binding proteins, the degree of opening/closing in MqnA appears to be different compared to nonenzymatic structural neighbors. A characteristic feature of VFT proteins is the ligand-mediated switching between an open ligand-free and a closed ligand-bound structure. The typical rotation would be about 15 degree without significant structural changes within the separate lobe domains. In contrast, the rotation angle between the two lobe domains accounts only for 7 degree. Deep cleft in center of enzyme. Opening and Closing of the VFT fold.
Chorismate dehydratase is also a homo dimer which means that both of its lobes have the same amount of amino acids and are structurally identical. The dimer is formed mostly by interactions of the N-terminal amino acids with helix α11 and the subsequent loop of the second molecule, as well as of amino acids 19 to 38 (containing β2 and α1) with the equivalent region of the second molecule. The dimer interface is distant from the active site and from the moving regions in VFT proteins, it’s not expected to influence catalysis.
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:https://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
