Structural basis of substrate specificity in human cytidine deaminase family APOBEC3s

Abstract

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Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state

“…While small molecule inhibitor development has not been successful, modified ssDNA oligonucleotides with the C 0 changed to 2′-deoxy-zebularine or 2′-deoxy-zebularine analogs have been shown to inhibit A3s 27, 28 although not with high potency. Zebularine was initially identified as a cytidine deaminase (CDA) inhibitor; however, CDA inhibitors do not inhibit A3s because, unlike CDAs that modify the single nucleoside, A3s deaminate cytidine in context of ssDNA 47 , suggesting they may require additional features beyond those needed for CDA binding. The high resolution (1.5 Å) A3G-CTD2:dZ-ssDNA structure we present here now helps understand both similarities between CDAs and A3s and the observed differences.…”

Unifying Different Cancer Theories in a Unique Tumour Model: Chronic Inflammation and Deaminases as Meeting Points

“…Similarly, the enhancement of APOBEC3A expression by pro-inflammatory factors, including IFNα, IFNγ, or LPs, has also been described [ 26 , 27 ]. Interestingly, it has been observed that APOBEC3A and APOBEC3B cytidine deaminases are the two members of this family of proteins that are the most frequently overexpressed in many types of malignancies [ 28 ]. Notably, some studies have revealed that APOBEC3A exhibits the highest enzymatic activity compared to other family components [ 7 ], suggesting the special importance of this molecule in cancer biology.…”

“…Regarding this idea, it has been observed that the APOBEC-mediated deamination preferentially occurs in TCW-specific DNA sequence motifs (“W” being any type of nucleotide) [ 80 ]. Furthermore, structural studies revealed substrate specificity differences between distinct members of the APOBEC3 group, such as APOBEC3A, 3B, or 3G [ 28 ], showing the existence of deamination motif heterogeneity regarding each deaminase. Therefore, an in-depth analysis of solid tumour biopsies could be proposed to establish a correlation between the activity of specific deaminases and the most probable mutational genome map.…”

“…To this end, the development of different molecular constructs combining the Crispr/Cas9 technology with DNA-based deaminases, such as AID or APOBECs with the objective of obtaining a targetable DNA based-editing tool has been studied [ 82 ]. However, there are still key limitations, such as off-target effects or wide editing windows [ 28 ]. Hence, a targetable DNA-editing approach seems suitable to be used in pre-clinical studies rather than in clinical practice in the near future.…”

The current toolbox for APOBEC drug discovery

“…In the case of double-domain enzymes, only the C-terminal domain is catalytically active; the N-terminal domain is similar to the catalytic domain in structure, but not in function, and is often referred to as 'pseudocatalytic ' [14]. A3 enzymes require a minimum 5-mer oligonucleotide for binding [15], where the ssDNA adopts a conformation that allows the target cytosine to access the active site (Figure 1C) [16][17][18][19]. Most A3 enzymes have a 5′-TC-3′ dinucleotide sequence preference [20][21][22][23][24][25][26]; A3G is the exception and prefers to deaminate cytosine in a 5′-CC-3′ motif [27][28][29].There is a large degree of sequence and structural conservation within and across the three Z-domains, but some unique features between the protein family members may be exploited to achieve selectivity during inhibitor development.…”