Oxanion hole
Encyclopedia
An oxyanion hole is a pocket in the structure of an enzyme
which stabilizes a deprotonated
oxygen
or alkoxide
, often by placing it close to positively charged residues. This can contribute to binding affinity in two ways:
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
which stabilizes a deprotonated
Deprotonation
Deprotonation is the removal of a proton from a molecule, forming the conjugate base.The relative ability of a molecule to give up a proton is measured by its pKa value. A low pKa value indicates that the compound is acidic and will easily give up its proton to a base...
oxygen
Oxygen
Oxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
or alkoxide
Alkoxide
An alkoxide is the conjugate base of an alcohol and therefore consists of an organic group bonded to a negatively charged oxygen atom. They can be written as RO−, where R is the organic substituent. Alkoxides are strong bases and, when R is not bulky, good nucleophiles and good ligands...
, often by placing it close to positively charged residues. This can contribute to binding affinity in two ways:
- It may directly stabilize the transition stateTransition stateThe transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest energy along this reaction coordinate. At this point, assuming a perfectly irreversible reaction, colliding reactant molecules will always...
of a reaction by stabilizing the anion (such as in the tetrahedral intermediateTetrahedral molecular geometryIn a tetrahedral molecular geometry a central atom is located at the center with four substituents that are located at the corners of a tetrahedron. The bond angles are cos−1 ≈ 109.5° when all four substituents are the same, as in CH4. This molecular geometry is common throughout the first...
formed in the proteolytic reaction catalyzed chymotrypsinChymotrypsinChymotrypsin is a digestive enzyme that can perform proteolysis. Chymotrypsin preferentially cleaves peptide amide bonds where the carboxyl side of the amide bond is a tyrosine, tryptophan, or phenylalanine. These amino acids contain an aromatic ring in their sidechain that fits into a...
) - It may allow for insertion or positioning of a substrate which would suffer from steric hindrance if it could not occupy the hole (such as BPG2,3-Bisphosphoglycerate2,3-Bisphosphoglyceric acid is a three-carbon isomer of the glycolytic intermediate 1,3-bisphosphoglyceric acid . 2,3-BPG is present in human red blood cells at approximately 5 mmol/L...
in hemoglobinHemoglobinHemoglobin is the iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates, with the exception of the fish family Channichthyidae, as well as the tissues of some invertebrates...
).