6M3L | pdb_00006m3l

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

• PDB DOI: https://doi.org/10.2210/pdb6M3L/pdb
• NAKB: 6M3L

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


• Deposited: 2020-03-04 Released: 2020-03-18 
• Deposition Author(s): Miyazono, K., Wang, D., Ito, T., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.306 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.283 (Depositor), 0.288 (DCC) 
• R-Value Observed: 
  0.284 (Depositor) 

Starting Model: experimental

Literature

Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.

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

(2020) Nucleic Acids Res 48: 5106-5118

• PubMed: 32232412 
• DOI: https://doi.org/10.1093/nar/gkaa184
• Primary Citation Related Structures: 
  6L2N, 6L2O, 6M3L


• 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.

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Organizational Affiliation: 
• Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo 113-8657, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.71 kDa 
• Atom Count: 3,342 
• Modeled Residue Count: 390 
• Deposited Residue Count: 463 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RE_R_Pab1 domain-containing protein	A, B	220	Pyrococcus abyssi GE5	Mutation(s): 2  Gene Names: PAB0105
UniProt
Find proteins for G8ZFZ3 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore G8ZFZ3  Go to UniProtKB:  G8ZFZ3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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')	C	23	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.306 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.283 (Depositor), 0.288 (DCC) 
• R-Value Observed: 0.284 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.153	α = 90
b = 84.153	β = 90
c = 140.53	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Miyazono, K., Wang, D., Ito, T., Tanokura, M.

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-04-01
  Changes: Derived calculations
• Version 1.2: 2020-04-15
  Changes: Database references
• Version 1.3: 2020-05-27
  Changes: Database references
• Version 1.4: 2023-11-29
  Changes: Data collection, Database references, Refinement description