Crystal Structure of the Zα Domain of the Human Editing Enzyme ADAR1 Bound to Left-Handed Z-DNA

Abstract

The editing enzyme double-stranded RNA adenosine deaminase includes a DNA binding domain, Zalpha, which is specific for left-handed Z-DNA. The 2.1 angstrom crystal structure of Zalpha complexed to DNA reveals that the substrate is in the left-handed Z conformation. The contacts between Zalpha and Z-DNA are made primarily with the "zigzag" sugar-phosphate backbone, which provides a basis for the specificity for the Z conformation. A single base contact is observed to guanine in the syn conformation, characteristic of Z-DNA. Intriguingly, the helix-turn-helix motif, frequently used to recognize B-DNA, is used by Zalpha to contact Z-DNA.

A 6 bp Z‐DNA hairpin binds two Zα domains from the human RNA editing enzyme ADAR1

“…The good agreement between these K d data and those obtained for wild-type ZK shows that the a¤nity of ZK to Z-DNA under reducing conditions is una¡ected by the C125S substitution. Moreover, the ZK domain forms a tight (ZK) 2 /hairpin complex without a disul¢de bond consistent with the absence of inter-ZK contacts in the crystal structure of the (ZK) 2 /Z-DNA complex [12]. However, under less strongly reducing conditions, the formation of a disul¢de bond at position 125 may tether two ZK domains.…”

“…It has been shown by several biochemical and spectroscopic studies in vitro [9^11], and by the crystal structure of ZK bound to substrate DNA [12] that the DNA complexed with ZK adopts the left-handed Z-conformation. Here we have used a de¢ned hairpin substrate, d(CG) 3 T 4 (CG) 3 , to determine the binding constant and stoichiometry of ZK bound to Z-DNA in solution.…”

The Zβ domain of human DAI binds to Z-DNA via a novel B-Z transition pathway

“…The crystal structure of the CG6-hZa ADAR1 complex [9] revealed that the side-chains of K169, R174, and K170 residues in hZa ADAR1 formed hydrogen bonds with three phosphate anions of the C3pG4pC5pG6 steps, respectively, in one strand of the CG6 duplex (Fig. 2C).…”

“…The crystal structure of the Za domain of human ADAR1 (hZa ADAR1 ) in complex with Z-DNA shows that two Za domains bind to each strand of double-stranded DNA and have twofold symmetry with respect to the DNA helical axis [9]. The Za domains of the yatapoxviral E3L (yabZa E3L ) and mouse DLM-1 (mZa DLM-1 ) show sequence homology to hZa ADAR1 and their overall structures and interactions with Z-DNA are similar to hZa A-DAR1 [10,11].…”

“…However, structural study with the Zb domain of human DAI (hZb DAI ) in complex with Z-DNA [12] suggests that hZb DAI shows unusual binding mode for Z-DNA recognition even though it has a structure that is similar to other Z-DNA binding proteins. The hZb DAI molecule shows hydrogen bond interactions with both strands of the Z-DNA duplex [12], whereas one molecule of hZa A-DAR1 interacts with only one strand in the Z-DNA duplex [9]. A previous NMR study assessed complex formation between hZa ADAR1 and a 6-base-paired (6-bp) DNA duplex, d(CGCGCG) 2 (referred to as CG6, Fig.…”