PDBsum entry 6hya

Membrane protein

PDB id: 6hya

Contents

Protein chains

311 a.a.

Ligands

LMT

Metals

_CL ×5

Waters ×1

PDB id:

6hya

Name:

Membrane protein

Title:

The glic pentameric ligand-gated ion channel mutant q193l

Structure:

Proton-gated ion channel. Chain: a, b, c, d, e. Fragment: unp residues 44-359. Synonym: glic,ligand-gated ion channel,lgic. Engineered: yes. Mutation: yes

Source:

Gloeobacter violaceus pcc 7421. Organism_taxid: 251221. Gene: glvi, glr4197. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

3.39Å R-factor: 0.185 R-free: 0.212

Authors:

H.D.Hu,M.Delarue

Key ref:

H.Hu et al. (2018). Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel. Proc Natl Acad Sci U S A, 115, E12172. PubMed id: 30541892 DOI: 10.1073/pnas.1813378116

Date:

19-Oct-18 Release date: 19-Dec-18

Protein chains

Q7NDN8  (GLIC_GLOVI) -  Proton-gated ion channel from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)

Seq: 359 a.a.

Struc: 311 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.1813378116

Proc Natl Acad Sci U S A 115:E12172 (2018)

PubMed id: 30541892

Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel.

H.Hu, K.Ataka, A.Menny, Z.Fourati, L.Sauguet, P.J.Corringer, P.Koehl, J.Heberle, M.Delarue.

ABSTRACT

The pentameric ligand-gated ion channel (pLGIC) from Gloeobacter violaceus (GLIC) has provided insightful structure-function views on the permeation process and the allosteric regulation of the pLGICs family. However, GLIC is activated by pH instead of a neurotransmitter and a clear picture for the gating transition driven by protons is still lacking. We used an electrostatics-based (finite difference Poisson-Boltzmann/Debye-Hückel) method to predict the acidities of all aspartic and glutamic residues in GLIC, both in its active and closed-channel states. Those residues with a predicted pK_a close to the experimental pH₅₀ were individually replaced by alanine and the resulting variant receptors were titrated by ATR/FTIR spectroscopy. E35, located in front of loop F far away from the orthosteric site, appears as the key proton sensor with a measured individual pK_a at 5.8. In the GLIC open conformation, E35 is connected through a water-mediated hydrogen-bond network first to the highly conserved electrostatic triad R192-D122-D32 and then to Y197-Y119-K248, both located at the extracellular domain-transmembrane domain interface. The second triad controls a cluster of hydrophobic side chains from the M2-M3 loop that is remodeled during the gating transition. We solved 12 crystal structures of GLIC mutants, 6 of them being trapped in an agonist-bound but nonconductive conformation. Combined with previous data, this reveals two branches of a continuous network originating from E35 that reach, independently, the middle transmembrane region of two adjacent subunits. We conclude that GLIC's gating proceeds by making use of loop F, already known as an allosteric site in other pLGICs, instead of the classic orthosteric site.