SNAP output for PDB entry 5yi3 [SNAP web server]

PDB-id

5yi3; SNAP-derived features in text and JSON formats; DNAproDB

Class

metal binding protein-DNA

Method

X-ray (2.9 Å)

Summary

Structure of lactococcus lactis zitr, c30s mutant in complex with DNA

Reference

Zhu R, Song Y, Liu H, Yang Y, Wang S, Yi C, Chen PR (2017): "Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation." Proc.Natl.Acad.Sci.USA, 114, 13661-13666. doi: 10.1073/pnas.1708563115.

Abstract

Metalloregulators allosterically control transcriptional activity through metal binding-induced reorganization of ligand residues and/or hydrogen bonding networks, while the coordination atoms on the same ligand residues remain seldom changed. Here we show that the MarR-type zinc transcriptional regulator ZitR switches one of its histidine nitrogen atoms for zinc coordination during the allosteric control of DNA binding. The Zn(II)-coordination nitrogen on histidine 42 within ZitR's high-affinity zinc site (site 1) switches from Nε2 to Nδ1 upon Zn(II) binding to its low-affinity zinc site (site 2), which facilitates ZitR's conversion from the nonoptimal to the optimal DNA-binding conformation. This histidine switch-mediated cooperation between site 1 and site 2 enables ZitR to adjust its DNA-binding affinity in response to a broad range of zinc fluctuation, which may allow the fine tuning of transcriptional regulation.