PDBsum entry 4q0r

Hydrolase/DNA

PDB id: 4q0r

Contents

Protein chains

293 a.a.

277 a.a.

DNA/RNA

Waters ×79

PDB id:

4q0r

Name:

Hydrolase/DNA

Title:

The catalytic core of rad2 (complex i)

Structure:

DNA repair protein rad2. Chain: a, b. Fragment: enzyme catalytic core, unp residues 2-111, unp residues 732-986. Engineered: yes. DNA (5'-d( Cp Tp Gp Ap Gp Tp Cp Ap Gp Ap Gp Cp Ap Ap A)- 3'). Chain: d. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: rad2, ygr258c. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes

Resolution:

2.75Å R-factor: 0.249 R-free: 0.310

Authors:

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

Key ref:

M.Miętus et al. (2014). Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding. Nucleic Acids Res, 42, 10762-10775. PubMed id: 25120270 DOI: 10.1093/nar/gku729

Date:

02-Apr-14 Release date: 27-Aug-14

Protein chain

P07276  (RAD2_YEAST) -  DNA repair protein RAD2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1031 a.a.

Struc: 293 a.a.*

Protein chain

P07276  (RAD2_YEAST) -  DNA repair protein RAD2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1031 a.a.

Struc: 277 a.a.*

* PDB and UniProt seqs differ at 137 residue positions (black crosses)

DNA/RNA chain

G-T-C-A 4 bases

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.1.-.-

DOI no: 10.1093/nar/gku729

Nucleic Acids Res 42:10762-10775 (2014)

PubMed id: 25120270

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

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

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.