4Q10 image
Deposition Date 2014-04-02
Release Date 2014-08-27
Last Version Date 2023-09-20
Entry Detail
PDB ID:
4Q10
Keywords:
Hydrolase/DNA
Title:
The catalytic core of Rad2 in complex with DNA substrate (complex IV)
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 559292)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.70 Å
R-Value Free:
0.28
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
C 1 2 1
4Q10 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA repair protein RAD2
Gene (Uniprot):RAD2
Chain IDs:A, B
Chain Length:365
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P07276 Pfam ID:PF00752, PF00867
Polymer Type:polydeoxyribonucleotide
Molecule: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')
Chain IDs:C
Chain Length:23
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule: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')
Chain IDs:D
Chain Length:23
Number of Molecules:1
Biological Source:
Ligand Molecules
CA
K
Primary Citation
Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding.
Nucleic Acids Res. 42 10762 10775 (2014)
PMID: 25120270 DOI: 10.1093/nar/gku729

Abstact

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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Disease

Primary Citation of related structures
4Q0W
4Q0Z
4Q10