PDBsum entry 6o8h

DNA binding protein/DNA

PDB id: 6o8h

Contents

Protein chain

571 a.a.

DNA/RNA

Ligands

SO4 ×2

Metals

_CL ×2

Waters ×158

PDB id:

6o8h

Name:

DNA binding protein/DNA

Title:

Crystal structure of uvrb mutant bound to duplex DNA

Structure:

Uvrabc system protein b. Chain: a. Synonym: protein uvrb,excinuclease abc subunit b. Engineered: yes. DNA (5'-d(p Cp Cp Ap Tp Cp Gp Cp Gp Cp Tp Ap Cp C)-3'). Chain: b. Engineered: yes. DNA (5'-d(p Ap Gp Cp Gp Cp Gp Ap Tp Gp Gp Ap Gp A)-3'). Chain: c.

Source:

Bacillus caldotenax. Organism_taxid: 1395. Gene: uvrb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

2.39Å R-factor: 0.230 R-free: 0.277

Authors:

S.-J.Lee,G.L.Verdine

Key ref:

S.J.Lee et al. (2019). Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System. Research (Wash D C), 2019, 5641746. PubMed id: 31549070 DOI: 10.34133/2019/5641746

Date:

10-Mar-19 Release date: 22-Jan-20

Protein chain

P56981  (UVRB_BACCA) -  UvrABC system protein B from Bacillus caldotenax

Seq: 658 a.a.

Struc: 571 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

DNA/RNA chains

C-C-A-T-C-G-C-G-C-T-A-C-C 13 bases

A-G-C-G-C-G-A-T-G-G-A-G-A 13 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.34133/2019/5641746

Research (Wash D C) 2019:5641746 (2019)

PubMed id: 31549070

Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System.

S.J.Lee, R.J.Sung, G.L.Verdine.

ABSTRACT

Nucleotide excision repair (NER) is an essential DNA repair system distinguished from other such systems by its extraordinary versatility. NER removes a wide variety of structurally dissimilar lesions having only their bulkiness in common. NER can also repair several less bulky nucleobase lesions, such as 8-oxoguanine. Thus, how a single DNA repair system distinguishes such a diverse array of structurally divergent lesions from undamaged DNA has been one of the great unsolved mysteries in the field of genome maintenance. Here we employ a synthetic crystallography approach to obtain crystal structures of the pivotal NER enzyme UvrB in complex with duplex DNA, trapped at the stage of lesion-recognition. These structures coupled with biochemical studies suggest that UvrB integrates the ATPase-dependent helicase/translocase and lesion-recognition activities. Our work also conclusively establishes the identity of the lesion-containing strand and provides a compelling insight to how UvrB recognizes a diverse array of DNA lesions.