6UKH

HhaI endonuclease in Complex with DNA in space group P41212 (pH 6.0)

Summary for 6UKH

• Entry DOI: 10.2210/pdb6ukh/pdb
• Descriptor: HhaI Restriction Endonuclease, DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*G)-3'), DNA (5'-D(*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3'), ... (5 entities in total)
• Functional Keywords: restriction, modification, protein-dna complex, iodine phasing, hydrolase-dna complex, hydrolase/dna
• Biological source: Haemophilus parahaemolyticus; More
• Total number of polymer chains: 3
• Total formula weight: 38618.80

Authors

Horton, J.R.,Cheng, X. (deposition date: 2019-10-04, release date: 2019-12-18, Last modification date: 2023-10-11)

Primary citation

Horton, J.R.,Yang, J.,Zhang, X.,Petronzio, T.,Fomenkov, A.,Wilson, G.G.,Roberts, R.J.,Cheng, X.
Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom.
Nucleic Acids Res., 48:1466-1478, 2020

PubMed Abstract: HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG↓C-3' in duplex DNA and cleaves ('↓') to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the 'PD-D/EXK' superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.

PubMed: 31879785
DOI: 10.1093/nar/gkz1195

Experimental method

X-RAY DIFFRACTION (2.82 Å)