4Q0Z | pdb_00004q0z

The catalytic core of Rad2 in complex with DNA substrate (complex III)

• PDB DOI: https://doi.org/10.2210/pdb4Q0Z/pdb
• NAKB: 4Q0Z

• Classification: Hydrolase/DNA
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-02 Released: 2014-08-27 
• Deposition Author(s): Mietus, M., Nowak, E., Jaciuk, M., Kustosz, P., Nowotny, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding.

Mietus, M., Nowak, E., Jaciuk, M., Kustosz, P., Studnicka, J., Nowotny, M.

(2014) Nucleic Acids Res 42: 10762-10775

• PubMed: 25120270 
• DOI: https://doi.org/10.1093/nar/gku729
• Primary Citation Related Structures: 
  4Q0R, 4Q0W, 4Q0Z, 4Q10


• PubMed Abstract: 
  

  Rad2/XPG belongs to the flap nuclease family and is responsible for a key step of the eukaryotic nucleotide excision DNA repair (NER) pathway. To elucidate the mechanism of DNA binding by Rad2/XPG, we solved crystal structures of the catalytic core of Rad2 in complex with a substrate. Rad2 utilizes three structural modules for recognition of the double-stranded portion of DNA substrate, particularly a Rad2-specific α-helix for binding the cleaved strand. The protein does not specifically recognize the single-stranded portion of the nucleic acid. Our data suggest that in contrast to related enzymes (FEN1 and EXO1), the Rad2 active site may be more accessible, which would create an exit route for substrates without a free 5' end.

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Organizational Affiliation: 
• Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland.
Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland [e-mail].

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 189.87 kDa 
• Atom Count: 13,433 
• Modeled Residue Count: 1,308 
• Deposited Residue Count: 1,528 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rad2p	A, B, E, F	365	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RAD2, YGR258C EC: 3.1
UniProt
Find proteins for P07276 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07276  Go to UniProtKB:  P07276

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3')	C, G	17	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3')	D, H	17	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	I [auth A], K [auth B], M [auth E], O [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	J [auth A], L [auth B], N [auth E], P [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.278	α = 90
b = 86.039	β = 110.95
c = 134.44	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Mietus, M., Nowak, E., Jaciuk, M., Kustosz, P., Nowotny, M.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2014-09-17
  Changes: Structure summary
• Version 1.2: 2014-10-01
  Changes: Database references
• Version 1.3: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2017-11-22
  Changes: Refinement description
• Version 1.5: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description