5IFF | pdb_00005iff

Crystal structure of R.PabI-nonspecific DNA complex

• PDB DOI: https://doi.org/10.2210/pdb5IFF/pdb
• NAKB: 5IFF

• Classification: HYDROLASE/DNA
• Organism(s): Pyrococcus abyssi GE5, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-02-26 Released: 2016-11-23 
• Deposition Author(s): Wang, D., Miyazono, K., Tanokura, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA.

Wang, D., Miyazono, K.I., Tanokura, M.

(2016) Sci Rep 6: 35197-35197

• PubMed: 27731370 
• DOI: https://doi.org/10.1038/srep35197
• Primary Citation Related Structures: 
  5IFF


• 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.

---

Organizational Affiliation: 
• Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.64 kDa 
• Atom Count: 4,044 
• Modeled Residue Count: 448 
• Deposited Residue Count: 460 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	220	Pyrococcus abyssi GE5	Mutation(s): 2  Gene Names: PAB0105
UniProt
Find proteins for Q9V2B6 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2B6  Go to UniProtKB:  Q9V2B6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*CP*TP*AP*GP*TP*TP*CP*GP*AP*AP*CP*TP*AP*GP*TP*GP*C)-3')	C	20	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.893	α = 90
b = 261.716	β = 90
c = 65.083	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Wang, D., Miyazono, K., Tanokura, M.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description