6DX0

Hermes transposase deletion dimer complex with (A/T) DNA

Summary for 6DX0

• Entry DOI: 10.2210/pdb6dx0/pdb
• Descriptor: Hermes transposase, DNA (5'-D(*AP*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3'), DNA (25-MER), ... (5 entities in total)
• Functional Keywords: transposase, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Musca domestica (House fly); More
• Total number of polymer chains: 4
• Total formula weight: 73790.23

Authors

Dyda, F.,Voth, A.R.,Hickman, A.B. (deposition date: 2018-06-28, release date: 2018-09-19, Last modification date: 2023-10-11)

Primary citation

Hickman, A.B.,Voth, A.R.,Ewis, H.,Li, X.,Craig, N.L.,Dyda, F.
Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase.
Nucleic Acids Res., 46:10286-10301, 2018

PubMed Abstract: Some DNA transposons relocate from one genomic location to another using a mechanism that involves generating double-strand breaks at their transposon ends by forming hairpins on flanking DNA. The same double-strand break mode is employed by the V(D)J recombinase at signal-end/coding-end junctions during the generation of antibody diversity. How flanking hairpins are formed during DNA transposition has remained elusive. Here, we describe several co-crystal structures of the Hermes transposase bound to DNA that mimics the reaction step immediately prior to hairpin formation. Our results reveal a large DNA conformational change between the initial cleavage step and subsequent hairpin formation that changes which strand is acted upon by a single active site. We observed that two factors affect the conformational change: the complement of divalent metal ions bound by the catalytically essential DDE residues, and the identity of the -2 flanking base pair. Our data also provides a mechanistic link between the efficiency of hairpin formation (an A:T basepair is favored at the -2 position) and Hermes' strong target site preference. Furthermore, we have established that the histidine residue within a conserved C/DxxH motif present in many transposase families interacts directly with the scissile phosphate, suggesting a crucial role in catalysis.

PubMed: 30239795
DOI: 10.1093/nar/gky838

Experimental method

X-RAY DIFFRACTION (2.9 Å)