Editing Active site (section)

==Binding site==
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{{Main|Binding site}}
Usually, an enzyme molecule has only one active site, and the active site fits with one specific type of substrate. An active site contains a binding site that binds the substrate and orients it for catalysis. The orientation of the substrate and the close proximity between it and the active site is so important that in some cases the enzyme can still function properly even though all other parts are [[mutation|mutated]] and lose function.<ref name="Dagmar">{{cite journal|vauthors=Dagmar R, Gregory A|date=2008|title=How Enzymes Work|journal=[[Science (journal)|Science]]|volume=320|issue=5882|pages=1428–1429|doi=10.1126/science.1159747|pmid=18556536|s2cid=43617575}}</ref>

Initially, the interaction between the active site and the substrate is non-covalent and transient. There are four important types of interaction that hold the substrate in a defined orientation and form an enzyme-substrate complex (ES complex): [[hydrogen bond]]s, [[Van der Waals force|van der Waals interactions]], [[hydrophobic interaction]]s and [[electrostatic|electrostatic force]] interactions.<ref name=":1">{{Cite book|url=https://enzimo.files.wordpress.com/2012/09/enzymes-a-practical-guide2.pdf|title=Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis|vauthors=Robert A|publisher=Wiley-Blackwell|year=2000|isbn=9780471359296|edition=2nd}}</ref>{{Rp|148}} The charge distribution on the substrate and active site must be complementary, which means all positive and negative charges must be cancelled out. Otherwise, there will be a repulsive force pushing them apart. The active site usually contains [[chemical polarity|non-polar]] amino acids, although sometimes polar amino acids may also occur.<ref name="google48"/> The binding of substrate to the binding site requires at least three contact points in order to achieve stereo-, regio-, and enantioselectivity. For example, [[alcohol dehydrogenase]] which catalyses the transfer of a [[hydride]] ion from [[ethanol]] to [[NADH|NAD<sup>+</sup>]] interacts with the substrate [[methyl group]], [[hydroxyl group]] and the pro-''(R)'' hydrogen that will be abstracted during the reaction.<ref name=":1" />{{Rp|149}}

In order to exert their function, enzymes need to assume their correct [[protein folding|protein fold]] (''native fold'') and [[tertiary structure]]. To maintain this defined three-dimensional structure, proteins rely on various types of interactions between their amino acid residues. If these interactions are interfered with, for example by extreme pH values, high temperature or high ion concentrations, this will cause the enzyme to [[Denaturation (biochemistry)|denature]] and lose its catalytic activity.{{citation needed|date=June 2024}}

A tighter fit between an active site and the substrate molecule is believed to increase the efficiency of a reaction. If the tightness between the active site of [[DNA polymerase]] and its substrate is increased, the fidelity, which means the correct rate of DNA replication will also increase.<ref name="Kool2002">{{Cite journal|vauthors=Kool ET|date=1984|title=Active site tightness and substrate fit in DNA replication|journal=[[Annual Review of Biochemistry]]|volume=71|pages=191–219|doi=10.1146/annurev.biochem.71.110601.135453|pmid=12045095}}</ref> Most enzymes have deeply buried active sites, which can be accessed by a substrate via access channels.<ref name=Pravda/>

There are three proposed models of how enzymes fit their specific substrate: the [[lock and key model]], the [[induced fit]] model, and the conformational selection model. The latter two are not mutually exclusive: conformational selection can be followed by a change in the enzyme's shape. Additionally, a protein may not wholly follow either model. Amino acids at the binding site of ubiquitin generally follow the induced fit model, whereas the rest of the protein generally adheres to conformational selection. Factors such as temperature likely influences the pathway taken during binding, with higher temperatures predicted to increase the importance of conformational selection and decrease that of induced fit.<ref name="CsermelyPalotai2010">{{cite journal|last1=Csermely|first1=Peter|last2=Palotai|first2=Robin|last3=Nussinov|first3=Ruth|title=Induced fit, conformational selection and independent dynamic segments: an extended view of binding events|journal=Trends in Biochemical Sciences|volume=35|issue=10|year=2010|pages=539–546|issn=0968-0004|doi=10.1016/j.tibs.2010.04.009|pmid=20541943|pmc=3018770|arxiv=1005.0348}}</ref>

===Lock and key hypothesis===

This concept was suggested by the 19th-century chemist [[Hermann Emil Fischer|Emil Fischer]]. He proposed that the active site and substrate are two stable structures that fit perfectly without any further modification, just like a key fits into a lock. If one substrate perfectly binds to its active site, the interactions between them will be strongest, resulting in high catalytic efficiency.

As time went by, limitations of this model started to appear. For example, the competitive [[enzyme inhibitor]] [[methylglucoside]] can bind tightly to the active site of [[4-alpha-glucanotransferase]] and perfectly fits into it. However, 4-alpha-glucanotransferase is not active on methylglucoside and no glycosyl transfer occurs. The Lock and Key hypothesis cannot explain this, as it would predict a high efficiency of methylglucoside glycosyl transfer due to its tight binding. Apart from competitive inhibition, this theory cannot explain the mechanism of action of [[Non-competitive inhibition|non-competitive inhibitors]] either, as they do not bind to the active site but nevertheless influence catalytic activity.<ref name="Daniel">{{cite journal|vauthors=Daniel E|date=1995|title=The Key–Lock Theory and the Induced Fit Theory|journal=[[Angewandte Chemie International Edition]]|volume=33|issue=2324|pages=2375–2378|doi=10.1002/anie.199423751}}</ref>

===Induced fit hypothesis===

[[Daniel E. Koshland Jr.|Daniel Koshland]]'s theory of enzyme-substrate binding is that the active site and the binding portion of the substrate are not exactly complementary.<ref name="Sullivan2008">{{Cite journal|vauthors=Sullivan SM|date=2008|title=Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection|journal=[[Proceedings of the National Academy of Sciences of the United States of America]]|volume=105|issue=37|pages=13829–13834|doi=10.1073/pnas.0805364105|pmc=2544539|pmid=18772387|bibcode=2008PNAS..10513829S|doi-access=free}}
</ref> The induced fit model is a development of the lock-and-key model and assumes that an active site is flexible and changes shape until the substrate is completely bound. This model is similar to a person wearing a glove: the glove changes shape to fit the hand. The enzyme initially has a conformation that attracts its substrate. Enzyme surface is flexible and only the correct catalyst can induce interaction leading to catalysis. Conformational changes may then occur as the substrate is bound. After the reaction products will move away from the enzyme and the active site returns to its initial shape. This hypothesis is supported by the observation that the entire protein domain could move several nanometers during catalysis. This movement of protein surface can create microenvironments that favour the catalysis.<ref name="Dagmar" />

===Conformational selection hypothesis===
This model suggests that enzymes exist in a variety of conformations, only some of which are capable of binding to a substrate. When a substrate is bound to the protein, the equilibrium in the conformational ensemble shifts towards those able to bind [[ligand (biochemistry)|ligand]]s (as enzymes with bound substrates are removed from the equilibrium between the free conformations).<ref name="Copeland2013">{{Cite book| publisher = John Wiley & Sons, Ltd| isbn = 978-1-118-54039-8| pages = 287–344| last = Copeland| first = Robert A.| title = Evaluation of Enzyme Inhibitors in Drug Discovery| chapter = Drug–Target Residence Time| date = 2013}}</ref>