7UI4

Crystal structure of the DNA preQ0 insertase DpdA

Summary for 7UI4

• Entry DOI: 10.2210/pdb7ui4/pdb
• Descriptor: DNA-guanine transglycosylase, ZINC ION (3 entities in total)
• Functional Keywords: 2'-deoxy-7-cyano-7-deazaguanosine, dpreq0, dna modification, dna-guanine transglycosylase, dna binding protein
• Biological source: Salmonella enterica subsp. enterica serovar Montevideo
• Total number of polymer chains: 1
• Total formula weight: 50410.28

Authors

Hung, S.-H.,Swairjo, M.A. (deposition date: 2022-03-28, release date: 2023-02-22, Last modification date: 2024-05-22)

Primary citation

Gedara, S.H.,Wood, E.,Gustafson, A.,Liang, C.,Hung, S.H.,Savage, J.,Phan, P.,Luthra, A.,de Crecy-Lagard, V.,Dedon, P.,Swairjo, M.A.,Iwata-Reuyl, D.
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system.
Nucleic Acids Res., 51:3836-3854, 2023

PubMed Abstract: The modified nucleosides 2'-deoxy-7-cyano- and 2'-deoxy-7-amido-7-deazaguanosine (dPreQ0 and dADG, respectively) recently discovered in DNA are the products of the bacterial queuosine tRNA modification pathway and the dpd gene cluster, the latter of which encodes proteins that comprise the elaborate Dpd restriction-modification system present in diverse bacteria. Recent genetic studies implicated the dpdA, dpdB and dpdC genes as encoding proteins necessary for DNA modification, with dpdD-dpdK contributing to the restriction phenotype. Here we report the in vitro reconstitution of the Dpd modification machinery from Salmonella enterica serovar Montevideo, the elucidation of the roles of each protein and the X-ray crystal structure of DpdA supported by small-angle X-ray scattering analysis of DpdA and DpdB, the former bound to DNA. While the homology of DpdA with the tRNA-dependent tRNA-guanine transglycosylase enzymes (TGT) in the queuosine pathway suggested a similar transglycosylase activity responsible for the exchange of a guanine base in the DNA for 7-cyano-7-deazaguanine (preQ0), we demonstrate an unexpected ATPase activity in DpdB necessary for insertion of preQ0 into DNA, and identify several catalytically essential active site residues in DpdA involved in the transglycosylation reaction. Further, we identify a modification site for DpdA activity and demonstrate that DpdC functions independently of DpdA/B in converting preQ0-modified DNA to ADG-modified DNA.

PubMed: 36928176
DOI: 10.1093/nar/gkad141

Experimental method

X-RAY DIFFRACTION (2.51 Å)