PDBsum entry 6fas

DNA binding protein

PDB id: 6fas

Contents

Protein chains

110 a.a.

DNA/RNA

Waters ×193

PDB id:

6fas

Name:

DNA binding protein

Title:

Crystal structure of val1 b3 domain in complex with cognate DNA

Structure:

B3 domain-containing transcription repressor val1. Chain: a, b. Synonym: protein high-level expression of sugar-inducible 2,protein vp1/abi3-like 1. Engineered: yes. Other_details: one cysteine forms an adduct with 2-mercaptoethanol. The resultant adduct is cme s,s-(2-hydroxyethyl)thiocysteine. DNA (5'-d( Ap Gp Cp Cp Ap Tp Gp Cp Ap Cp Cp G)-3'). Chain: c, e.

Source:

Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Gene: val1, hsi2, at2g30470, t6b20.17. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

1.90Å R-factor: 0.174 R-free: 0.217

Authors:

G.Sasnauskas

Key ref:

G.Sasnauskas et al. (2018). Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1. Nucleic Acids Res, 46, 4316-4324. PubMed id: 29660015

Date:

17-Dec-17 Release date: 18-Apr-18

Protein chains

Q8W4L5  (VAL1_ARATH) -  B3 domain-containing transcription repressor VAL1 from Arabidopsis thaliana

Seq: 790 a.a.

Struc: 110 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

A-G-C-C-A-T-G-C-A-C-C-G 12 bases

C-G-G-T-G-C-A-T-G-G-C-T 12 bases

A-G-C-C-A-T-G-C-A-C-C-G 12 bases

C-G-G-T-G-C-A-T-G-G-C-T 12 bases

Nucleic Acids Res 46:4316-4324 (2018)

PubMed id: 29660015

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.

G.Sasnauskas, K.Kauneckaite, V.Siksnys.

ABSTRACT

Arabidopsis thaliana requires a prolonged period of cold exposure during winter to initiate flowering in a process termed vernalization. Exposure to cold induces epigenetic silencing of the FLOWERING LOCUS C (FLC) gene by Polycomb group (PcG) proteins. A key role in this epigenetic switch is played by transcriptional repressors VAL1 and VAL2, which specifically recognize Sph/RY DNA sequences within FLC via B3 DNA binding domains, and mediate recruitment of PcG silencing machinery. To understand the structural mechanism of site-specific DNA recognition by VAL1, we have solved the crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence 5'-CATGCA-3'/5'-TGCATG-3'. We find that VAL1-B3 makes H-bonds and van der Waals contacts to DNA bases of all six positions of the canonical Sph/RY element. In agreement with the structure, in vitro DNA binding studies show that VAL1-B3 does not tolerate substitutions at any position of the 5'-TGCATG-3' sequence. The VAL1-B3-DNA structure presented here provides a structural model for understanding the specificity of plant B3 domains interacting with the Sph/RY and other DNA sequences.