Structural Biochemistry/Deaminase

=Deaminase=

Deaminase is an enzyme that is involved in the process of Deamination in which the process removes an amine group (NH2) from a molecule through hydrolysis. The enzyme will usually only remove an amine group from extra proteins and this occurs in the liver or kidneys. This enzyme is very beneficial to the body because it allows deamination to follow through. Without Deamination waste (usually Nitrogen waste) may not be able to leave the body. The Nitrogen waste is expelled through urination which is a result of the removal of the amine group by deaminase. In addition to removing wastes, deamination using deaminase also allows the body to convert the extra amino groups removed from proteins into more beneficial sources that the body may use in all other sorts reactions. Thus, this contributes to the balance of the body's metabolism in that it allows the body to not accumulate a surplus amount of certain molecules which may lead to diseases or even cancer.

Deamination can be very deleterious process. For example, by deaminating adenine, hypoxanthine is formed. This product pairs with guanine and cytosine. Even though this process in the long run does not cause any change in protein formation, if it does, then the result may be disastrous. There are many kinds of deaminases. Deamination can happen in guanine and cytosine as well.



APOBEC3G (A3G)
APOBEC3G, known as A3G, belongs to a family of cytidine deaminases named for the first known enzyme to possess the capacity for site-specific cytidine to uridine deamination of B messenger RNA. A3G has been demonstrated to be significant in the cellular defense against the progression of Human immunodeficiency virus (HIV).

Antiviral Mechanisms
The A3G deaminase dependent and independent antiviral mechanisms are known to induce mutations in the HIV viral genome.

In the deaminase dependent mechanism, this occurs due to the ability of A3G to catalyze zinc-dependent hydrolytic deamination of deoxycytidine, instead forming deoxyuridine in HIV DNA. Mutation distribution and frequency within the viral DNA is determined by a variety of factors including the availability of ssDNA (single-strand DNA) and the speed of nucleotide addition (3' to 5' processivity).

As for the deaminase-independent mechanism, A3G is suspected of containing both N-terminal and C-terminal zinc-dependent deaminase (ZDD) folds. ZDD consists of a sequence which is known to comprise five anti-parallel beta sheets which are supported and maintained by two alpha helices (which position cysteine and histidine residues for the coordination binding of a zinc atom, a water molecule, and a glutamic acid residue, all necessary for the conversion of cytidine and deoxycitidine to uridine and deoxyuridine, respectively. It has been demonstrated that such deaminase activity is limited to C-terminal ZDD folds.

"Double Agent" Function in Cellular Defense
In the cellular defense against the HIV virus, APOBEC3G (A3G) serves to induce mutations in the viral genome, effectively preventing high-fidelity replication and deleterious gene-expression in non-viral cells. However, the HIV-encoded protein Vif (short for Viral Infectivity Factor), is known to allow for the infection of cells even in the presence of A3G. This occurs because Vif triggers the destruction of A3G, preventing its incorporation into growing viral strands. This effectively makes impotent the ability of A3G to hypermutate HIV ssDNA during the process of reverse transcription necessary for viral genome replication. However, while A3G is known to serve as an antiviral factor through both Deaminase-dependent and deaminase-independent pathways, it has been suggested that the mutagenic effects induced in the viral genome are insufficient so as to inactive and make harmless the HIV genome. As such, A3G may induce diversification of viral DNA strands, resulting in new, more virulent strains of viral genome. In light of this knowledge, the level of A3G-induced mutation has been discussed relative to whether it benefits or destroys viral factors. While research has not yielded the levels of A3G activity necessary to reinforce antiviral efforts, it has been suggested that inhibition of Vif would yield long-term detrimental effects, ultimately aiding viral diversification. Alternatively, inhibiting A3G activity and allowing Vif to destroy A3G cells may reduce the emergency of viral diversity and accompanying resistance.

Resource
Biochemistry 7th edition by Jeremy M. Berg

Smith, Harold. "APOBEC3G: a double agent in defense." Trends in Biochemical Science. 2011 May;36(5):239-44. Epub 2011 Jan 14.

Sumayao, Marco, and Jenn Walker. "What Is Deamination?" WiseGeek. Conjecture, 2003. Web. 20 Nov. 2012. .