5ZJ4

Guanine-specific ADP-ribosyltransferase

Summary for 5ZJ4

• Entry DOI: 10.2210/pdb5zj4/pdb
• Descriptor: ADP-ribosyltransferase, (4S)-2-METHYL-2,4-PENTANEDIOL (3 entities in total)
• Functional Keywords: adp-ribosyltransferase, transferase
• Biological source: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
• Total number of polymer chains: 4
• Total formula weight: 73915.49

Authors

Yoshida, T.,Tsuge, H. (deposition date: 2018-03-19, release date: 2018-08-08, Last modification date: 2024-10-23)

Primary citation

Yoshida, T.,Tsuge, H.
Substrate N2atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP.
J. Biol. Chem., 293:13768-13774, 2018

PubMed Abstract: ScARP from the bacterium belongs to the pierisin family of DNA-targeting ADP-ribosyltransferases (ARTs). These enzymes ADP-ribosylate the N amino groups of guanine residues in DNA to yield N-(ADP-ribos-1-yl)-2'-deoxyguanosine. Although the structures of pierisin-1 and Scabin were revealed recently, the substrate recognition mechanisms remain poorly understood because of the lack of a substrate-binding structure. Here, we report the apo structure of ScARP and of ScARP bound to NADH and its GDP substrate at 1.50 and 1.57 Å resolutions, respectively. The bound structure revealed that the guanine of GDP is trapped between -ribose of NADH and Trp-159. Interestingly, N and N of guanine formed hydrogen bonds with the OE1 and NE2 atoms of Gln-162, respectively. We directly observed that the ADP-ribosylating toxin turn-turn (ARTT)-loop, including Trp-159 and Gln-162, plays a key role in the specificity of DNA-targeting, guanine-specific ARTs as well as protein-targeting ARTs such as the C3 exoenzyme. We propose that the ARTT-loop recognition is a common substrate-recognition mechanism in the pierisin family. Furthermore, this complex structure sheds light on similarities and differences among two subclasses that are distinguished by conserved structural motifs: H-Y-E in the ARTD subfamily and R-S-E in the ARTC subfamily. The spatial arrangements of the electrophile and nucleophile were the same, providing the first evidence for a common reaction mechanism in these ARTs. ARTC (including ScARP) uses the ARTT-loop for substrate recognition, whereas ARTD (represented by Arr) uses the C-terminal helix instead of the ARTT-loop. These observations could help inform efforts to improve ART inhibitors.

PubMed: 30072382
DOI: 10.1074/jbc.AC118.004412

Experimental method

X-RAY DIFFRACTION (1.49739273546 Å)