Structural Investigations on the Interactions between Cytidine Deaminase Human APOBEC3G and DNA

Abstract

Human APOBEC3G (A3G) inhibits the replication of human immunodeficiency virus‐1 by deaminating cytidine at the 3′‐end in the target motif 5′‐CCC‐3′ in viral cDNA during reverse transcription. It in vitro deaminates two consecutive cytidines in a 3′‐>5′ order. Although a crystal structure of the A3G catalytic domain (A3G‐CD2) with DNA was reported, it is unknown why residues involved in enzymatic reaction are distributed widely. Here, we introduced an iodine atom into the C‐5 position of cytidine (dC6I) in DNA 5′‐ATTC4C5C6IA7ATT‐3′ (TCCC6I). It switches the deamination sequence preference from CCC to TCC, although small dC6I deamination was observed. Solution structures of A3G‐CD2 in complexes with products DNA TCUC6I and TCUU6I indicate that the substrate DNA binds A3G‐CD2 in TCC and CCC modes. The dC6 deamination correlates with the 4th base type. The CCC mode favours dC6 deamination, while the TCC mode results in dC5 deamination. These studies present an extensive basis to design inhibitors to impede viral evolvability.

Two different kinds of interaction modes of deaminase APOBEC3A with single‐stranded DNA in solution detected by nuclear magnetic resonance

“…The structure of inactive pseudo-catalytic rhesus macaque A3G-NTD (i.e., rA3G-NTD) in complex with poly-dT ssDNA (PDB code 5K83) 29 reveals that only one deoxythymidine is in a shallow cleft close to the pseudo-catalytic zinc-binding motif. The structures of A3G-CD2 in complex with two deamination product DNA strands containing 5-iodinated CUC I and CCU I motifs (PDB codes 6K3J and 6K3K) 30 imply the structural basis of the two DNA binding modes responsible for cytidine deamination in TCC and CCC motifs catalyzed by A3G, respectively. The 10-site A3G-CD2 variant (i.e., P200A, L234K, N236A, C243A, P247K, Q318K, F310K, C321A, Q322A, and C356A, termed as A3G-CTD2) was reported to have much stronger binding affinity to DNA and higher catalytic efficiency than wild-type A3G-CD2.…”

A3G‐induced mutations show a low prevalence and exhibit plus‐strand regional distribution in hepatitis B virus DNA from patients with non‐hepatocellular carcinoma (HCC) and HCC

“…A3G preferentially targets the second cytosine deamination of 5′ CC3′, 7,9,23,28 or the third cytosine deamination of 5′CCC3′ 20,21,24 on single stranded DNA (with the deamination site underlined). We first…”

“…The CCC → CCK mutation is the A3G signature mutation. [19][20][21]24 The ratio (r) of the rate of C → K mutation in the CCCH context to the C → K mutation rate in the CH context can be used as a parameter to reflect the prevalence of A3G signature mutations. Thus, we calculated the r-value of CCCH → CCKH in population HBV DNA to reveal the distribution characteristics of A3G-induced mutations.…”

The current toolbox for APOBEC drug discovery

“…Incubation of A3A with several slightly different ssDNA substrates allowed researchers to map key A3A-ssDNA interactions and provide parameters for computational models. In addition, combinations of similar 2DNMR methods as described previously have been used to solve solution structures of A3A [106], A3B [107], and A3G [86,[108][109][110][111]. These NMR assays have potential to aid A3 lead discovery and optimization given their high orthogonality to the other assays reviewed here.…”