PDBsum entry 6jw3

DNA binding protein/DNA

PDB id: 6jw3

Contents

Protein chains

497 a.a.

DNA/RNA

Waters ×10

PDB id:

6jw3

Name:

DNA binding protein/DNA

Title:

Degenerate rvd rg forms a distinct loop conformation

Structure:

Tal effector. Chain: a, b, e, h. Engineered: yes. DNA (5'-d( Tp Gp Tp Cp Cp Cp Tp Tp (5Cm) p Gp Cp Gp Tp Cp Tp Cp T)-3'). Chain: i, c, f, k. Engineered: yes. DNA (5'- d( Ap Gp Ap Gp Ap Cp Gp Cp Gp Ap Ap Gp Gp Gp Ap Cp A)-3').

Source:

Xanthomonas campestris pv. Armoraciae. Organism_taxid: 329463. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

3.10Å R-factor: 0.244 R-free: 0.278

Authors:

L.Liu,C.Yi

Key ref:

L.Liu et al. (2020). Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors. J Mol Biol, 432, 1035-1047. PubMed id: 31863750 DOI: 10.1016/j.jmb.2019.11.023

Date:

18-Apr-19 Release date: 22-Apr-20

Protein chains

Q3ZD72  (Q3ZD72_XANCA) -  Hax3 from Xanthomonas campestris pv. armoraciae

Seq: 960 a.a.

Struc: 497 a.a.*

* PDB and UniProt seqs differ at 23 residue positions (black crosses)

DNA/RNA chains

T-G-T-C-C-C-T-T-5CM-G-C-G-T-C-T-C-T 17 bases

A-G-A-G-A-C-G-C-G-A-A-G-G-G-A-C-A 17 bases

T-G-T-C-C-C-T-T-5CM-G-C-G-T-C-T-C-T 17 bases

A-G-A-G-A-C-G-C-G-A-A-G-G-G-A-C-A 17 bases

T-G-T-C-C-C-T-T-5CM-G-C-G-T-C-T-C-T 17 bases

A-G-A-G-A-C-G-C-G-A-A-G-G-G-A-C-A 17 bases

T-G-T-C-C-C-T-T-5CM-G-C-G-T-C-T-C-T 17 bases

A-G-A-G-A-C-G-C-G-A-A-G-G-G-A-C-A 17 bases

DOI no: 10.1016/j.jmb.2019.11.023

J Mol Biol 432:1035-1047 (2020)

PubMed id: 31863750

Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors.

L.Liu, Y.Zhang, M.Liu, W.Wei, C.Yi, J.Peng.

ABSTRACT

Transcription activator-like effectors (TALEs) recognize DNA through repeat-variable diresidues (RVDs), and TALE-DNA interactions are sensitive to DNA modifications. Our previous study deciphered the recognition of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) by TALEs. Here, we report seven crystal structures of TALE-DNA complexes. The 5mC-specific RVD HA recognizes 5mC through van der Waals interactions and exhibits highly similar loop conformation to natural RVDs. The degenerate RVD RG contacts 5mC and 5hmC via van der Waals interactions as well; however, its loop conformation differs significantly. The loop conformations of universal RVD R* and 5hmC-specific RVD Q* are similar to that of RG, while the interactions of R* with C/5mC/5hmC and Q* with 5hmC are mediated by waters. Together, our findings illustrate the molecular basis for the specific recognition of 5mC and 5hmC by multiple noncanonical TALEs and provide insights into the plasticity of the TALE RVD loops.