PDBsum entry 4yir

DNA binding protein/DNA

PDB id: 4yir

Contents

Protein chains

499 a.a.

53 a.a.

DNA/RNA

PDB id:

4yir

Name:

DNA binding protein/DNA

Title:

Crystal structure of rad4-rad23 crosslinked to an undamaged DNA

Structure:

DNA repair protein rad4. Chain: a. Engineered: yes. Uv excision repair protein rad23. Chain: x. Engineered: yes. DNA (5'-d( Tp Tp Gp Ap Cp Tp Cp (G47) p Ap Cp Ap Tp Cp Cp Cp Cp Cp Gp Cp Tp Ap Cp Ap A)-3'). Chain: w.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: rad4, yer162c. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: high five cells (bti-tn-5b1-4).

Resolution:

3.05Å R-factor: 0.197 R-free: 0.253

Authors:

J.-H.Min,X.Chen,Y.Kim

Key ref:

X.Chen et al. (2015). Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat Commun, 6, 5849. PubMed id: 25562780 DOI: 10.1038/ncomms6849

Date:

02-Mar-15 Release date: 11-Mar-15

Supersedes:

4u29

Protein chain

P14736  (RAD4_YEAST) -  DNA repair protein RAD4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 754 a.a.

Struc: 499 a.a.*

Protein chain

P32628  (RAD23_YEAST) -  UV excision repair protein RAD23 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 398 a.a.

Struc: 53 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

T-T-G-A-C-T-C-G47-A-C-A-T-C-C-C-C-C-G-C-T-A-C-A-A 24 bases

A-T-T-G-T-A-G-C-G-G-G-G-A-T-G-T-C-G-A-G-T-C-A 23 bases

DOI no: 10.1038/ncomms6849

Nat Commun 6:5849 (2015)

PubMed id: 25562780

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.

X.Chen, Y.Velmurugu, G.Zheng, B.Park, Y.Shim, Y.Kim, L.Liu, B.Van Houten, C.He, A.Ansari, J.H.Min.

ABSTRACT

The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.