6M3L

Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex

Summary for 6M3L

• Entry DOI: 10.2210/pdb6m3l/pdb
• Related: 6L2N 6L2O
• Descriptor: RE_R_Pab1 domain-containing protein, DNA (5'-D(*CP*GP*CP*AP*TP*CP*GP*AP*TP*TP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*GP*CP*G)-3') (2 entities in total)
• Functional Keywords: glycosylase, hydrolase-dna complex, hydrolase/dna
• Biological source: Pyrococcus abyssi (strain GE5 / Orsay); More
• Total number of polymer chains: 3
• Total formula weight: 57713.85

Authors

Miyazono, K.,Wang, D.,Ito, T.,Tanokura, M. (deposition date: 2020-03-04, release date: 2020-03-18, Last modification date: 2023-11-29)

Primary citation

Miyazono, K.I.,Wang, D.,Ito, T.,Tanokura, M.
Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.
Nucleic Acids Res., 48:5106-5118, 2020

PubMed Abstract: R.PabI is a restriction DNA glycosylase that recognizes the sequence 5'-GTAC-3' and hydrolyses the N-glycosidic bond of adenine in the recognition sequence. R.PabI drastically bends and unwinds the recognition sequence of double-stranded DNA (dsDNA) and flips the adenine and guanine bases in the recognition sequence into the catalytic and recognition sites on the protein surface. In this study, we determined the crystal structure of the R.PabI-dsDNA complex in which the dsDNA is drastically bent by the binding of R.PabI but the base pairs are not unwound. This structure is predicted to be important for the indirect readout of the recognition sequence by R.PabI. In the complex structure, wedge loops of the R.PabI dimer are inserted into the minor groove of dsDNA to stabilize the deformed dsDNA structure. A base stacking is distorted between the two wedge-inserted regions. R.PabI is predicted to utilize the distorted base stacking for the detection of the recognition sequence.

PubMed: 32232412
DOI: 10.1093/nar/gkaa184

Experimental method

X-RAY DIFFRACTION (2.75 Å)