PDBsum entry 3n1h

DNA binding protein

PDB id: 3n1h

Contents

Protein chain

161 a.a. *

Ligands

PO4 ×2

Waters ×69

* Residue conservation analysis

PDB id:

3n1h

Name:

DNA binding protein

Title:

Crystal structure of stwhy2

Structure:

Stwhy2. Chain: a. Fragment: whirly domain. Engineered: yes

Source:

Solanum tuberosum. Potato. Organism_taxid: 4113. Strain: kennebec. Gene: stwhy2. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.206 R-free: 0.251

Authors:

L.Cappadocia,N.Brisson,J.Sygusch

Key ref:

L.Cappadocia et al. (2010). Crystal structures of DNA-Whirly complexes and their role in Arabidopsis organelle genome repair. Plant Cell, 22, 1849-1867. PubMed id: 20551348

Date:

15-May-10 Release date: 11-Aug-10

Protein chain

D9J034  (WHY2_SOLTU) -  Single-stranded DNA-binding protein WHY2, mitochondrial from Solanum tuberosum

Seq: 238 a.a.

Struc: 161 a.a.

Plant Cell 22:1849-1867 (2010)

PubMed id: 20551348

Crystal structures of DNA-Whirly complexes and their role in Arabidopsis organelle genome repair.

L.Cappadocia, A.Maréchal, J.S.Parent, E.Lepage, J.Sygusch, N.Brisson.

ABSTRACT

DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial genome stability in plants, little is known about the mechanisms of DNA repair in these organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteins from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant organelle genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.