Sandbox Reserved 1544: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Tom Gluick (talk | contribs) |
Yechan Kang (talk | contribs) No edit summary |
||
| (29 intermediate revisions by 4 users not shown) | |||
| Line 1: | Line 1: | ||
{{ Sandbox_Reserved_GGC_BHCM4100_1}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | {{ Sandbox_Reserved_GGC_BHCM4100_1}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
<Structure load='1ege' size='350' side='right' caption='Acyl-CoA Dehydrogenase' scene='49/491924/Cv/1'> | |||
__TOC__ | |||
== Function == | == Function == | ||
3. | |||
The first reaction in β-oxidation, or fatty acid metabolism, is the catalyzation of the ester bond (C2 and C3) of the substrate Acyl-CoA.<ref name="Berg">Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002. Chapter 22, Fatty Acid Metabolism. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21173/</ref> This is accomplished through <scene name='49/491924/Cv/1'>acyl-CoA dehydrogenase</scene> and its cofactor <scene name='49/491924/Cv/3'>FAD</scene>.<ref name="Berg"/> ACDH is classified according to its length of its substrates: short (SCAD), medium (MCAD), very and very long-chain (VLCAD).<ref name="Lee"/> | |||
== Disease == | == Disease == | ||
Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is a disorder that affects fatty acid oxidation and can be characterized by a hypoglycemic crisis during times of increased stress.<ref name="Lee">Lee, H.-J. K.; Wang, M.; Paschke, R.; Nandy, A.; Ghisla, S.; Kim, J.-J. P. Crystal Structures of the Wild Type and the Glu376Gly/Thr255Glu Mutant of Human Medium-Chain Acyl-CoA Dehydrogenase: Influence of the Location of the Catalytic Base on Substrate Specificity†. https://pubs.acs.org/doi/pdf/10.1021/bi9607867 (accessed May 5, 2019).</ref> Expression of MCADD results in a decrease of ketone production and an increase in medium-chain fatty acid concentration.<ref name="Lee"/> MCADD is a disorder inherited genetically through an autosomal recessive trait, and it is caused by mutations in the medium-chain acyl- CoA dehydrogenase (ACADM) gene.<ref name="Lee"/> The ACADM gene is located on chromosome 1p31.<ref name="Lee"/> There are over 90 different ACADM gene mutations known so far, most of which are missense mutations.<ref name="Lee"/> The disorder can lead to symptoms such as a loss in appetite as well as vomiting and diarrhea.<ref name="Lee"/> This can result in accumulated concentrations of acylcarnitine, which can be potentially toxic.<ref name="Lee"/> People who are affected and not diagnosed are at a high risk of dying or experiencing permanent neurological damage during their first metabolic crisis.<ref name="Lee"/> To prevent such events, immediate care should follow catabolic stress and fasting should be averted.<ref name="Lee"/> Individuals living with MCADD are asymptomatic up until there is an increased demand for energy followed by a prolonged time of fasting.<ref name="Lee"/> Newborn screening is now widely implemented through the use of liquid chromatography-tandem mass spectrometry.<ref name="Lee"/> | |||
== Relevance == | == Relevance == | ||
'''Fatty Acid Metabolism''' | |||
Acyl-CoA dehydrogenase is the first enzyme used to metabolize fatty acids.<ref name="Berg"/> | |||
In the first step, fatty acyl-CoA is converted to trans-Δ<sup>2</sup>-enoyl-CoA via <scene name='49/491924/Cv/1'>acyl-CoA dehydrogenase</scene> with the help of <scene name='49/491924/Cv/3'>FAD</scene>, releasing FADH<sub>2</sub> as a byproduct.<ref name="Berg"/> | |||
In the second step, trans-Δ<sup>2</sup>-enoyl-CoA is converted to 3-L-hydroxyacyl-CoA via enoyl-CoA hydratase with the help of H<sub>2</sub>O.<ref name="Berg"/> | |||
In the third step, 3-L-hydroxyacyl-CoA is converted to β-ketoacyl-CoA via 3-hydroxyacyl-CoA dehydrogenase with the help of NAD<sup>+</sup>, releasing NADH + H<sup>+</sup> as a byproduct.<ref name="Berg"/> | |||
In the fourth step, β-ketoacyl-CoA is converted to another fatty acyl-CoA with two less carbons or finishes the cycle as Acetyl-CoA if there are two remaining carbons.<ref name="Berg"/> This reaction occurs via β-ketohiolase with the help of CoA-SH.<ref name="Berg"/> | |||
The four steps are repeated until the fatty acid is metabolized to less than or equal to 3 carbons.<ref name="Berg"/> | |||
== Structural highlights == | == Structural highlights == | ||
'''1ege''' is a <scene name='49/491924/Cv/2'>4 chain structure</scene>, distinguished by the letters A, B, C, and D. Each chain is composed of the ligand FAD and Coenzyme A. | |||
'''Catalytic Residues''' | |||
Glu255 is responsible for the catalytic activity of mutant Medium Chain Acyl-CoA Dehydrogenase (MCADH).<ref name="Lee"/> It can be in “active” or “resting” states.<ref name="Lee"/> It is mostly in the “resting” state, due to its ability to hydrogen bond with Glu99.<ref name="Lee"/> | |||
Long Chain Acyl-CoA Dehydrogenase (LCADH) and Isovaleryl-CoA Dehydrogenase (IVDH) have a higher catalytic activity than MCADH because they have serine and glycine in their 99 position, respectively.<ref name="Lee"/> Neither of these amino acids can form hydrogen bonds, so the Glu255 is in the “active state.”<ref name="Lee"/> The catalytic residue of LCADH is Glu261; the catalytic residue of IVDH is Glu254.<ref name="Lee"/> | |||
Glu376 is the amino acid responsible for catalytic activity of the wild type.<ref name="Lee"/> | |||
'''Significance of the Positions of Glutamate on the <scene name='80/806430/Wildtype/1'>Wild Type</scene> (Glu376) and Mutant (Glu255)''' | |||
The distance between the donor proton and the base that attacks the donor proton affect the catalytic activity of the carboxylate base of the glutamates.<ref name="Lee"/> The distance between the proton and glutamates carboxylates are more than 4.0 A.<ref name="Lee"/> | |||
Glu376 would conform so that its carboxylate oxygen lies close to the proton (2.4A).<ref name="Lee"/> | |||
Glu255 has a smaller catalytic activity because is over 4.0 A away from the proton.<ref name="Lee"/> It is thought that due to MCADH’s flexibility at Gly376, Glu255’s carboxylate oxygen will be closer to the donor proton.<ref name="Lee"/> | |||
When both Glu255 and Glu376 are available to the Thr255Glu mutant, Glu376 can act as a catalytic residue and Glu255 adopts the “resting” conformation.<ref name="Lee"/> This is expected given that the kinetic parameters of the mutant and its optimum substrates (C8- and C10-CoA) are similar to those of the wild type enzyme.<ref name="Lee"/> The substrates (in both wild type and MLCADH) with alkyl chain lengths that are longer than C12-CoA can form multiple conformers at its ω-end in the active site cavity.<ref name="Lee"/> However, this is not the case for the Glu/Glu mutant due to the glutamate side chains.<ref name="Lee"/> This steric hindrance prevents the binding of the long substrate in an orientation that would allow catalysis to occur.<ref name="Lee"/> | |||
'''Solvent Accessibility and Oxygen Reactivity.''' | |||
In the MLCADH, the bore of the active site cavity at its midsection is wider and allows the longer substrate to adopt multiple conformations at its ω-end.<ref name="Lee"/> This better accommodates the MLCADH for catalysis than the wild type.<ref name="Lee"/> The wider bore also allows bulkier substrates to bind to the enzyme more easily.<ref name="Lee"/> Having a larger active site allows more solvent molecules, which leads to larger amounts of molecular oxygen, which is becomes readily available to reduced Flavin.<ref name="Lee"/> This difference in width (8.5 Å vs 5.1 Å) allows for the oxidation of the reduced Flavin to occur somewhere between 10 to 100 times faster than the wild type.<ref name="Lee"/> Ligands that lack the carbonyl oxygen are much less effective at protecting the reduced enzyme flavin toward molecular oxygen.<ref name="Lee"/> | |||
== References == | == References == | ||
<references/> | <references/> | ||
