Editing Enzyme (section)

== Mechanism ==
[[File:Enzyme structure.svg|thumb|400px|Organisation of [[protein structure|enzyme structure]] and [[lysozyme]] example. Binding sites in blue, catalytic site in red and [[peptidoglycan]] substrate in black. ({{PDB|9LYZ}})|alt=Lysozyme displayed as an opaque globular surface with a pronounced cleft which the substrate depicted as a stick diagram snuggly fits into.]]

=== Substrate binding ===
Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what [[substrate (biochemistry)|substrates]] they bind and then the chemical reaction catalysed. [[Chemical specificity|Specificity]] is achieved by binding pockets with complementary shape, charge and [[hydrophilic]]/[[hydrophobic]] characteristics to the substrates. Enzymes can therefore distinguish between very similar substrate molecules to be [[chemoselectivity|chemoselective]], [[regioselectivity|regioselective]] and [[stereospecificity|stereospecific]].<ref>{{cite journal | vauthors = Jaeger KE, Eggert T | title = Enantioselective biocatalysis optimized by directed evolution | journal = Current Opinion in Biotechnology | volume = 15 | issue = 4 | pages = 305–313 | date = August 2004 | pmid = 15358000 | doi = 10.1016/j.copbio.2004.06.007 }}</ref>

Some of the enzymes showing the highest specificity and accuracy are involved in the copying and [[Gene expression|expression]] of the [[genome]]. Some of these enzymes have "[[Proofreading (biology)|proof-reading]]" mechanisms. Here, an enzyme such as [[DNA polymerase]] catalyzes a reaction in a first step and then checks that the product is correct in a second step.<ref>{{cite journal | vauthors = Shevelev IV, Hübscher U | title = The 3' 5' exonucleases | journal = Nature Reviews. Molecular Cell Biology | volume = 3 | issue = 5 | pages = 364–376 | date = May 2002 | pmid = 11988770 | doi = 10.1038/nrm804 | s2cid = 31605786 }}</ref> This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases.<ref name = "Stryer_2002"/>{{rp|5.3.1}} Similar proofreading mechanisms are also found in [[RNA polymerase]],<ref>{{cite journal | vauthors = Zenkin N, Yuzenkova Y, Severinov K | title = Transcript-assisted transcriptional proofreading | journal = Science | volume = 313 | issue = 5786 | pages = 518–520 | date = July 2006 | pmid = 16873663 | doi = 10.1126/science.1127422 | s2cid = 40772789 | bibcode = 2006Sci...313..518Z }}</ref> [[aminoacyl tRNA synthetase]]s<ref>{{cite journal | vauthors = Ibba M, Soll D | title = Aminoacyl-tRNA synthesis | journal = Annual Review of Biochemistry | volume = 69 | pages = 617–650 | year = 2000 | pmid = 10966471 | doi = 10.1146/annurev.biochem.69.1.617 }}</ref> and [[ribosome]]s.<ref>{{cite journal | vauthors = Rodnina MV, Wintermeyer W | title = Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms | journal = Annual Review of Biochemistry | volume = 70 | pages = 415–435 | year = 2001 | pmid = 11395413 | doi = 10.1146/annurev.biochem.70.1.415 }}</ref>

Conversely, some enzymes display [[enzyme promiscuity]], having broad specificity and acting on a range of different physiologically relevant substrates. Many enzymes possess small side activities which arose fortuitously (i.e. [[Neutral evolution|neutrally]]), which may be the starting point for the evolutionary selection of a new function.<ref name=Tawfik10>{{cite journal | vauthors = Khersonsky O, Tawfik DS | title = Enzyme promiscuity: a mechanistic and evolutionary perspective | journal = Annual Review of Biochemistry | volume = 79 | pages = 471–505 | year = 2010 | pmid = 20235827 | doi = 10.1146/annurev-biochem-030409-143718 }}</ref><ref>{{cite journal | vauthors = O'Brien PJ, Herschlag D | title = Catalytic promiscuity and the evolution of new enzymatic activities | journal = Chemistry & Biology | volume = 6 | issue = 4 | pages = R91–R105 | date = April 1999 | pmid = 10099128 | doi = 10.1016/S1074-5521(99)80033-7 | doi-access = free }}</ref>

[[File:Hexokinase induced fit.svg|alt=Hexokinase displayed as an opaque surface with a pronounced open binding cleft next to unbound substrate (top) and the same enzyme with more closed cleft that surrounds the bound substrate (bottom)|thumb|400px|Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex. [[Hexokinase]] has a large induced fit motion that closes over the substrates [[adenosine triphosphate]] and [[xylose]]. Binding sites in blue, substrates in black and [[magnesium|Mg<sup>2+</sup>]] cofactor in yellow. ({{PDB|2E2N}}, {{PDB2|2E2Q}})]]

==== "Lock and key" model ====
To explain the observed specificity of enzymes, in 1894 [[Hermann Emil Fischer|Emil Fischer]] proposed that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another.<ref>{{cite journal | vauthors = Fischer E | year = 1894 | title = Einfluss der Configuration auf die Wirkung der Enzyme | language = de | trans-title = Influence of configuration on the action of enzymes | journal=Berichte der Deutschen Chemischen Gesellschaft zu Berlin | volume = 27 | issue = 3 | pages = 2985–93 | url = http://gallica.bnf.fr/ark:/12148/bpt6k90736r/f364.chemindefer|doi=10.1002/cber.18940270364 }} From page 2992: ''"Um ein Bild zu gebrauchen, will ich sagen, dass Enzym und Glucosid wie Schloss und Schlüssel zu einander passen müssen, um eine chemische Wirkung auf einander ausüben zu können."'' (To use an image, I will say that an enzyme and a glucoside [i.e., glucose derivative] must fit like a lock and key, in order to be able to exert a chemical effect on each other.)</ref> This is often referred to as "the lock and key" model.<ref name="Stryer_2002" />{{rp|8.3.2}} This early model explains enzyme specificity, but fails to explain the stabilization of the transition state that enzymes achieve.<ref name="Cooper_2000">{{cite book | author = Cooper GM | title = The Cell: a Molecular Approach | date = 2000 | publisher = ASM Press | location = Washington (DC ) | isbn = 0-87893-106-6 | edition = 2nd | chapter = Chapter 2.2: The Central Role of Enzymes as Biological Catalysts | chapter-url = https://www.ncbi.nlm.nih.gov/books/NBK9921/ | url-access = registration | url = https://archive.org/details/cell00geof }}</ref>

==== Induced fit model ====
In 1958, [[Daniel E. Koshland, Jr.|Daniel Koshland]] suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continuously reshaped by interactions with the substrate as the substrate interacts with the enzyme.<ref>{{cite journal | vauthors = Koshland DE | title = Application of a Theory of Enzyme Specificity to Protein Synthesis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 44 | issue = 2 | pages = 98–104 | date = February 1958 | pmid = 16590179 | pmc = 335371 | doi = 10.1073/pnas.44.2.98 | doi-access = free | bibcode = 1958PNAS...44...98K }}</ref> As a result, the substrate does not simply bind to a rigid active site; the amino acid [[Side chain|side-chains]] that make up the active site are molded into the precise positions that enable the enzyme to perform its catalytic function. In some cases, such as [[glycosidases]], the substrate [[molecule]] also changes shape slightly as it enters the active site.<ref>{{cite journal | vauthors = Vasella A, Davies GJ, Böhm M | title = Glycosidase mechanisms | journal = Current Opinion in Chemical Biology | volume = 6 | issue = 5 | pages = 619–629 | date = October 2002 | pmid = 12413546 | doi = 10.1016/S1367-5931(02)00380-0 }}</ref> The active site continues to change until the substrate is completely bound, at which point the final shape and charge distribution is determined.<ref>{{cite book | vauthors = Boyer R | title = Concepts in Biochemistry | edition = 2nd | publisher = John Wiley & Sons, Inc. | location = New York, Chichester, Weinheim, Brisbane, Singapore, Toronto. | isbn = 0-470-00379-0 | pages=137–8 | chapter = Chapter 6: Enzymes I, Reactions, Kinetics, and Inhibition | year = 2002 | oclc = 51720783 }}</ref>
Induced fit may enhance the fidelity of molecular recognition in the presence of competition and noise via the [[conformational proofreading]] mechanism.<ref>{{cite journal | vauthors = Savir Y, Tlusty T | title = Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition | journal = PLOS ONE | volume = 2 | issue = 5 | pages = e468 | date = May 2007 | pmid = 17520027 | pmc = 1868595 | doi = 10.1371/journal.pone.0000468 | veditors = Scalas E | doi-access = free | bibcode = 2007PLoSO...2..468S }}</ref>

=== Catalysis ===

{{See also|Enzyme catalysis|Transition state theory}}

Enzymes can accelerate reactions in several ways, all of which lower the [[activation energy]] (ΔG<sup>‡</sup>, [[Gibbs free energy]])<ref name="Fersht_1985">{{cite book | author = Fersht A | title = Enzyme Structure and Mechanism | publisher = W.H. Freeman | location = San Francisco | year = 1985 | pages = 50–2 | isbn = 978-0-7167-1615-0}}</ref>
# By stabilizing the transition state:
#* Creating an environment with a charge distribution complementary to that of the transition state to lower its energy<ref>{{cite journal | vauthors = Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MH | title = Electrostatic basis for enzyme catalysis | journal = Chemical Reviews | volume = 106 | issue = 8 | pages = 3210–3235 | date = August 2006 | pmid = 16895325 | doi = 10.1021/cr0503106 }}</ref>
# By providing an alternative reaction pathway:
#* Temporarily reacting with the substrate, forming a covalent intermediate to provide a lower energy transition state<ref>{{cite book | vauthors = Cox MM, Nelson DL | title = Lehninger Principles of Biochemistry | date = 2013 | publisher = W.H. Freeman | location = New York, N.Y. | isbn = 978-1464109621 | edition = 6th | chapter = Chapter 6.2: How enzymes work | page = 195 }}</ref>
# By destabilizing the substrate ground state:
#* Distorting bound substrate(s) into their transition state form to reduce the energy required to reach the transition state<ref name=PMID12947189>{{cite journal | vauthors = Benkovic SJ, Hammes-Schiffer S | title = A perspective on enzyme catalysis | journal = Science | volume = 301 | issue = 5637 | pages = 1196–1202 | date = August 2003 | pmid = 12947189 | doi = 10.1126/science.1085515 | s2cid = 7899320 | bibcode = 2003Sci...301.1196B }}</ref>
#* By orienting the substrates into a productive arrangement to reduce the reaction [[entropy]] change<ref>{{cite book | author = Jencks WP | title = Catalysis in Chemistry and Enzymology | publisher = Dover | location = Mineola, N.Y | year = 1987 | isbn = 978-0-486-65460-7 }}</ref> (the contribution of this mechanism to catalysis is relatively small)<ref>{{cite journal | vauthors = Villa J, Strajbl M, Glennon TM, Sham YY, Chu ZT, Warshel A | title = How important are entropic contributions to enzyme catalysis? | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 97 | issue = 22 | pages = 11899–11904 | date = October 2000 | pmid = 11050223 | pmc = 17266 | doi = 10.1073/pnas.97.22.11899 | doi-access = free | bibcode = 2000PNAS...9711899V }}</ref>
Enzymes may use several of these mechanisms simultaneously. For example, [[protease]]s such as [[trypsin]] perform covalent catalysis using a [[catalytic triad]], stabilize charge build-up on the transition states using an [[oxyanion hole]], complete [[hydrolysis]] using an oriented water substrate.<ref>{{cite journal | vauthors = Polgár L | title = The catalytic triad of serine peptidases | journal = Cellular and Molecular Life Sciences | volume = 62 | issue = 19–20 | pages = 2161–2172 | date = October 2005 | pmid = 16003488 | doi = 10.1007/s00018-005-5160-x | s2cid = 3343824 | pmc = 11139141 }}</ref>

=== Dynamics ===

{{See also|Protein dynamics}}

Enzymes are not rigid, static structures; instead they have complex internal dynamic motions – that is, movements of parts of the enzyme's structure such as individual amino acid residues, groups of residues forming a [[turn (biochemistry)|protein loop]] or unit of [[protein secondary structure|secondary structure]], or even an entire [[protein domain]]. These motions give rise to a [[conformational ensemble]] of slightly different structures that interconvert with one another at [[thermodynamic equilibrium|equilibrium]]. Different states within this ensemble may be associated with different aspects of an enzyme's function. For example, different conformations of the enzyme [[dihydrofolate reductase]] are associated with the substrate binding, catalysis, cofactor release, and product release steps of the catalytic cycle,<ref>{{cite journal | vauthors = Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK | title = Protein conformational populations and functionally relevant substates | journal = Accounts of Chemical Research | volume = 47 | issue = 1 | pages = 149–156 | date = January 2014 | pmid = 23988159 | doi = 10.1021/ar400084s | osti = 1565147 }}</ref> consistent with [[catalytic resonance theory]]. The transitions between the different conformations during the catalytic cycle involve internal [[Viscoelasticity|viscoelatic]] motion that is facilitated by high-[[Strain (mechanics)|strain]] regions where amino acids are rearranged.<ref>{{Cite journal |last=Weinreb |first=Eyal |last2=McBride |first2=John M. |last3=Siek |first3=Marta |last4=Rougemont |first4=Jacques |last5=Renault |first5=Renaud |last6=Peleg |first6=Yoav |last7=Unger |first7=Tamar |last8=Albeck |first8=Shira |last9=Fridmann-Sirkis |first9=Yael |last10=Lushchekina |first10=Sofya |last11=Sussman |first11=Joel L. |last12=Grzybowski |first12=Bartosz A. |last13=Zocchi |first13=Giovanni |last14=Eckmann |first14=Jean-Pierre |last15=Moses |first15=Elisha |date=2025-03-28 |title=Enzymes as viscoelastic catalytic machines |url=https://www.nature.com/articles/s41567-025-02825-9 |journal=Nature Physics |language=en |pages=1–12 |doi=10.1038/s41567-025-02825-9 |issn=1745-2481|url-access=subscription }}</ref>

=== Substrate presentation ===
[[Substrate presentation]] is a process where the enzyme is sequestered away from its substrate. Enzymes can be sequestered to the plasma membrane away from a substrate in the nucleus or cytosol.<ref>{{cite journal | vauthors = Agrawal D, Budakoti M, Kumar V | title = Strategies and tools for the biotechnological valorization of glycerol to 1, 3-propanediol: Challenges, recent advancements and future outlook | journal = Biotechnology Advances | volume = 66 | pages = 108177 | date = September 2023 | pmid = 37209955 | doi = 10.1016/j.biotechadv.2023.108177 | hdl = 1826/19759 }}</ref> Or within the membrane, an enzyme can be sequestered into lipid rafts away from its substrate in the disordered region. When the enzyme is released it mixes with its substrate. Alternatively, the enzyme can be sequestered near its substrate to activate the enzyme. For example, the enzyme can be soluble and upon activation bind to a lipid in the plasma membrane and then act upon molecules in the plasma membrane.<ref>{{cite journal | vauthors = Selvy PE, Lavieri RR, Lindsley CW, Brown HA | title = Phospholipase D: enzymology, functionality, and chemical modulation | journal = Chemical Reviews | volume = 111 | issue = 10 | pages = 6064–6119 | date = October 2011 | pmid = 21936578 | pmc = 3233269 | doi = 10.1021/cr200296t }}</ref>

=== Allosteric modulation ===
{{main|Allosteric regulation}}

Allosteric sites are pockets on the enzyme, distinct from the active site, that bind to molecules in the cellular environment. These molecules then cause a change in the conformation or dynamics of the enzyme that is transduced to the active site and thus affects the reaction rate of the enzyme.<ref>{{cite journal | vauthors = Tsai CJ, Del Sol A, Nussinov R | title = Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms | journal = Molecular BioSystems | volume = 5 | issue = 3 | pages = 207–216 | date = March 2009 | pmid = 19225609 | pmc = 2898650 | doi = 10.1039/b819720b }}</ref> In this way, allosteric interactions can either inhibit or activate enzymes. Allosteric interactions with metabolites upstream or downstream in an enzyme's metabolic pathway cause [[feedback]] regulation, altering the activity of the enzyme according to the [[Flux (metabolism)|flux]] through the rest of the pathway.<ref>{{cite journal | vauthors = Changeux JP, Edelstein SJ | title = Allosteric mechanisms of signal transduction | journal = Science | volume = 308 | issue = 5727 | pages = 1424–1428 | date = June 2005 | pmid = 15933191 | doi = 10.1126/science.1108595 | s2cid = 10621930 | bibcode = 2005Sci...308.1424C }}</ref>