3WAZ | pdb_00003waz

Crystal structure of a restriction enzyme PabI in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb3WAZ/pdb
• NAKB: 3WAZ

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


• Deposited: 2013-05-10 Released: 2014-01-29 
• Deposition Author(s): Miyazono, K., Miyakawa, T., Ito, T., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.194 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi.

Miyazono, K., Furuta, Y., Watanabe-Matsui, M., Miyakawa, T., Ito, T., Kobayashi, I., Tanokura, M.

(2014) Nat Commun 5: 3178-3178

• PubMed: 24458096 
• DOI: https://doi.org/10.1038/ncomms4178
• Primary Citation Related Structures: 
  3WAZ


• PubMed Abstract: 
  

  Restriction-modification systems consist of genes that encode a restriction enzyme and a cognate methyltransferase. Thus far, it was believed that restriction enzymes are sequence-specific endonucleases that introduce double-strand breaks at specific sites by catalysing the cleavages of phosphodiester bonds. Here we report that based on the crystal structure and enzymatic activity, one of the restriction enzymes, R.PabI, is not an endonuclease but a sequence-specific adenine DNA glycosylase. The structure of the R.PabI-DNA complex shows that R.PabI unwinds DNA at a 5'-GTAC-3' site and flips the guanine and adenine bases out of the DNA helix to recognize the sequence. R.PabI catalyses the hydrolysis of the N-glycosidic bond between the adenine base and the sugar in the DNA and produces two opposing apurinic/apyrimidinic (AP) sites. The opposing AP sites are cleaved by heat-promoted β elimination and/or by endogenous AP endonucleases of host cells to introduce a double-strand break.

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Organizational Affiliation: 
• Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
1] Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Tokyo 108-8639, Japan [2] Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.
1] Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Tokyo 108-8639, Japan [2].
1] Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Tokyo 108-8639, Japan [2] Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan [3] Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 108-8639, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 62.98 kDa 
• Atom Count: 4,347 
• Modeled Residue Count: 473 
• Deposited Residue Count: 480 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	220	Pyrococcus abyssi GE5	Mutation(s): 1  Gene Names: PYRAB01580, 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*TP*AP*GP*CP*TP*GP*TP*(ORP)P*CP*AP*GP*CP*TP*AP*TP*GP*C)-3')	C, D	20	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	E [auth A], F [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.194 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.508	α = 90
b = 151.402	β = 90
c = 187.697	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Miyazono, K., Miyakawa, T., Ito, T., Tanokura, M.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Database references, Derived calculations, Source and taxonomy
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description