5IFF

Crystal structure of R.PabI-nonspecific DNA complex

Summary for 5IFF

• Entry DOI: 10.2210/pdb5iff/pdb
• Descriptor: Uncharacterized protein, DNA (5'-D(*GP*CP*AP*CP*TP*AP*GP*TP*TP*CP*GP*AP*AP*CP*TP*AP*GP*TP*GP*C)-3') (3 entities in total)
• Functional Keywords: restriction enzyme, dna glycosylase, hydrolase-dna complex, hydrolase/dna
• Biological source: Pyrococcus abyssi; More
• Total number of polymer chains: 3
• Total formula weight: 56642.15

Authors

Wang, D.,Miyazono, K.,Tanokura, M. (deposition date: 2016-02-26, release date: 2016-11-23, Last modification date: 2023-11-08)

Primary citation

Wang, D.,Miyazono, K.I.,Tanokura, M.
Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA.
Sci Rep, 6:35197-35197, 2016

PubMed Abstract: R.PabI is a type II restriction enzyme that recognizes the 5'-GTAC-3' sequence and belongs to the HALFPIPE superfamily. Although most restriction enzymes cleave phosphodiester bonds at specific sites by hydrolysis, R.PabI flips the guanine and adenine bases of the recognition sequence out of the DNA helix and hydrolyzes the N-glycosidic bond of the flipped adenine in a similar manner to DNA glycosylases. In this study, we determined the structure of R.PabI in complex with double-stranded DNA without the R.PabI recognition sequence by X-ray crystallography. The 1.9 Å resolution structure of the complex showed that R.PabI forms a tetrameric structure to sandwich the double-stranded DNA and the tetrameric structure is stabilized by four salt bridges. DNA binding and DNA glycosylase assays of the R.PabI mutants showed that the residues that form the salt bridges (R70 and D71) are essential for R.PabI to find the recognition sequence from the sea of nonspecific sequences. R.PabI is predicted to utilize the tetrameric structure to bind nonspecific double-stranded DNA weakly and slide along it to find the recognition sequence.

PubMed: 27731370
DOI: 10.1038/srep35197

Experimental method

X-RAY DIFFRACTION (1.9 Å)