6M3L image
Deposition Date 2020-03-04
Release Date 2020-03-18
Last Version Date 2023-11-29
Entry Detail
PDB ID:
6M3L
Keywords:
HYDROLASE/DNA
Title:
Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex
Biological Source:
Source Organism:
Pyrococcus abyssi (strain GE5 / Orsay) (Taxon ID: 272844)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.75 Å
R-Value Free:
0.30
R-Value Work:
0.28
R-Value Observed:
0.28
Space Group:
P 32 2 1
6M3L validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RE_R_Pab1 domain-containing protein
Gene (Uniprot):PAB0105
Mutations:Y65F, K151A
Chain IDs:A, B
Chain Length:220
Number of Molecules:2
Biological Source:Pyrococcus abyssi (strain GE5 / Orsay)
UniProt ID:G8ZFZ3 Pfam ID:PF09522 EC:3.1.21.4
Polymer Type:polydeoxyribonucleotide
Molecule: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')
Chain IDs:C
Chain Length:23
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
NA
Primary Citation
Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.
Nucleic Acids Res. 48 5106 5118 (2020)
PMID: 32232412 DOI: 10.1093/nar/gkaa184

Abstact

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.

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Disease

Primary Citation of related structures
6L2O
6L2N