AlkD (Alkylpurine glycosylase D) is an

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

belonging to a family of DNA glycosylases that are involved in

DNA repair DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA dam ...

. It was discovered by a team of Norwegian biologists from

Oslo Oslo ( , , or ; sma, Oslove) is the capital and most populous city of Norway. It constitutes both a county and a municipality. The municipality of Oslo had a population of in 2022, while the city's greater urban area had a population of ...

in 2006. It was isolated from a soil-dwelling

Gram-positive bacteria In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. Gram-positive bact ...

'' Bacillus cereus'', along with another enzyme AlkC. AlkC and AlkD are most probably derived from the same protein as indicated by their close resemblance. They are also found in other

prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...

s. Among

eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...

s, they are found only in the single-celled species only, such as '' Entamoeba histolytica'' and '' Dictyostelium discoideum''. The enzyme specifically targets 7mG (methyl-

guanine Guanine () ( symbol G or Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is called ...

) in the DNA, and is, therefore, unique among DNA glycosylases. It can also act on other methylpurines with less affinity. It indicates that the enzyme is specific for locating and cutting ( excision) of chemically modified bases from DNA, exactly at 7mG, whenever there are errors in replication. It accelerates the rate of 7mG hydrolysis 100-fold over the spontaneous depurination. Thus, it protects the genome from harmful changes induced by chemical and environmental agents. Its

crystal structure In crystallography, crystal structure is a description of the ordered arrangement of atoms, ions or molecules in a crystal, crystalline material. Ordered structures occur from the intrinsic nature of the constituent particles to form symmetric pat ...

was described in 2008. It is the first HEAT repeat protein identified to interact with

nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...

s or to contain enzymatic activity.

Structure

AlkD is made up of 237

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...

s, and has a molecular size of 25 kDa. It is composed of a tandem array of helical repeats reminiscent of HEAT motifs, which are known to facilitate protein-protein interactions and have not yet been associated with DNA binding or catalytic activity. It is a single-stranded protein with α-helical domain. The entire protein domain is composed of HEAT repeat domains, similar to those found in other proteins. Twelve of the fourteen helices (αA-αN) pair in an antiparallel pattern, and form six tandemly repeated α-α motifs, such as αA/αC, αD/αE, αF/αG, αH/αI, αJ/αK, and αL/αM. These helical repeats are stacked into a superhelical solenoid in which helices B, C, E, G, I, K and M form a concave surface with an

aromatic In chemistry, aromaticity is a chemical property of cyclic ( ring-shaped), ''typically'' planar (flat) molecular structures with pi bonds in resonance (those containing delocalized electrons) that gives increased stability compared to satur ...

cleft at its center. Residues within this cleft are crucial for the base excision activity. The concave surface is positively charged and is presumed to be the binding site of DNA, as well as for protection against bacterial sensitivity to

alkylating Alkylation is the transfer of an alkyl group from one molecule to another. The alkyl group may be transferred as an alkyl carbocation, a free radical, a carbanion, or a carbene (or their equivalents). Alkylating agents are reagents for effecting ...

agents.

Mechanism of action

AlkD has a unique mechanism for base excision in DNA. Instead of interacting directly with the damaged (alkylated) DNA portion, it acts on the nearby undamaged region. It then induces flipping of the alkylated and opposing base accompanied by DNA stack compression. The exposed DNA portion can then be enzymatically removed, by

hydrolysis Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution reaction, substitution, elimination reaction, elimination, and solvation reactions in which water ...

of the 7mG.

References

{{Reflist DNA repair Hydrolases