4Q10

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: 10.1093/nar/gku729
  • Primary Citation of Related Structures:  
    4Q10, 4Q0R, 4Q0W, 4Q0Z

  • 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/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.


    Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland mnowotny@iimcb.gov.pl.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein RAD2A, B365Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD2YGR258C
EC: 3.1
Find proteins for P07276 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07276 
Go to UniProtKB:  P07276
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*TP*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*TP*TP*TP*T)-3')C23N/A
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*TP*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*TP*TP*TP*T)-3')D23N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], G [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A], H [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.68α = 90
b = 97.958β = 96.41
c = 112.038γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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