Molecular Playground/DnaK
From Proteopedia
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One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.
Molecular Playground banner: DnaK, a central hub in maintaining proteostasis in E. coli
The E. coli Hsp70, DnaK, is a crucial protein chaperone whose function is to reduce bind exposed hydrohpobic residues of unfolded proteins, which prevents aggregation and rescues the nascent chain from kinetic traps along the folding pathway. Hsp70 protein chaperones switch between an , low-substrate affinity form and an , high substrate affinity form during their allosteric cycle.[1] [2] Hsp70 protein chaperones are ubiquitously found in almost all known organisms and cell types and represent a potential target for anti-cancer and neurodegenerative therapies.[3]
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Structure
DnaK is a 638 residue protein of approximately 70 kDa. The protein can be thought to be made up of two domains, the N-terminal nucleotide-binding domain () (residues 1-388), the C-terminal substrate-binding domain () (residues 393-638), which are divided by the (residues 389-392, shown in purple). The NBD is further divided into four subdomains: (residues 1-37, 112-184, 363-383, shown in red), (residues 38-111, shown in green), (residues 185-227, 310-362, shown in gold), and (residues 228-309, shown in purple). The SBD of DnaK consists of a (residues 393-507), an (residues 508-605), and a disordered C-terminal tail (not shown due to lack of available crystal structure). [4]
Function
Upon ATP binding, the subdomains rotate relative to each other and induce a conformational change in the NBD (compare the NBD to the form (shown with ATP bound).
When ATP binds the NBD, the resulting allosteric signal induces a conformational change in the SBD as well. Compare the form of the SBD (when the NBD binds ATP) and the form of the SBD (when the NBD binds ADP).
DHFR catalyzes the reduction of 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate using reduced Nicotinamide Adenine Dinucleotide Phosphate (NADPH). This system has been key model to decipher enzyme catalysis and the intermediates of the catalytic cycle have been identified by crystallography. CPMG relaxation NMR experiments have also revealed that intermediates in the catalytic cycle exist in equilibrium with the preceding or following intermediate. Thus the binding of ligands seems to happen via a conformational selection rather than the traditional view of induced fit which is used to explain conformation change on ligand binding.[5]. shows the ligands Dihydrofolate and NADP+ positioned in the active site cleft.[6]
Drug Target
Since DHFR is so critically positioned in the metabolic homeostasis of all organsims it has been the target of choice for anti microbial and anti cancer therapy. Inhibitors of this enzyme are essentially folate mimics, methotrexate which was first designed to inhibit and used as therapy for cancer and autoimmune disorders. Another folate mimic Trimethoprim was developed as an anti bacterial agent, having much more binding specificity to bacterial DHFR than its mammalian counterpart. Both drugs bind in the active site of the enzyme and are irreversibly bound thus ablating enzyme activity.[7] [8].
3D structures of DHFR
See Also
The wikipedia link on DHFR is also pretty useful for a general background.[[9]]
References
1. Kityk, R. et al. Mol Cell 2012
2. Bertelsen EB. et al. Proc Natl Acad Sci USA 2009
3. Broer L. et al. j Alzherimers Dis 2011
4. Zuiderweg ER. et al. Top Curr Chem 2013
5. Dauber-Osguthorpe P et al. Proteins 1988
6. Cody V. et al. Acta Crystallogr D Biol Crystallogr. 2005
