PDBsum entry 5vrf

Membrane protein

PDB id: 5vrf

Contents

Protein chains

282 a.a.

Metals

_ZN ×8

PDB id:

5vrf

Name:

Membrane protein

Title:

Cryoem structure of the zinc transporter yiip from helical crystals

Structure:

Cadmium and zinc efflux pump fief. Chain: b, a. Engineered: yes

Source:

Shewanella oneidensis mr-1. Organism_taxid: 211586. Strain: mr-1. Gene: fief, so_4475. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Authors:

N.Coudray,M.Lopez-Redondo,Z.Zhang,J.Alexopoulos,D.L.Stokes, Transcontinental Em Initiative For Membrane Protein Structure (Temimps)

Key ref:

M.L.Lopez-Redondo et al. (2018). Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP. Proc Natl Acad Sci U S A, 115, 3042-3047. PubMed id: 29507252

Date:

10-May-17 Release date: 14-Mar-18

Protein chains

Q8E919  (Q8E919_SHEON) -  Cation-efflux pump FieF from Shewanella oneidensis (strain MR-1)

Seq: 296 a.a.

Struc: 282 a.a.

Enzyme reactions

• Enzyme class: E.C.?

Proc Natl Acad Sci U S A 115:3042-3047 (2018)

PubMed id: 29507252

Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP.

M.L.Lopez-Redondo, N.Coudray, Z.Zhang, J.Alexopoulos, D.L.Stokes.

ABSTRACT

YiiP is a dimeric antiporter from the cation diffusion facilitator family that uses the proton motive force to transport Zn²⁺across bacterial membranes. Previous work defined the atomic structure of an outward-facing conformation, the location of several Zn²⁺binding sites, and hydrophobic residues that appear to control access to the transport sites from the cytoplasm. A low-resolution cryo-EM structure revealed changes within the membrane domain that were associated with the alternating access mechanism for transport. In the current work, the resolution of this cryo-EM structure has been extended to 4.1 Å. Comparison with the X-ray structure defines the differences between inward-facing and outward-facing conformations at an atomic level. These differences include rocking and twisting of a four-helix bundle that harbors the Zn²⁺transport site and controls its accessibility within each monomer. As previously noted, membrane domains are closely associated in the dimeric structure from cryo-EM but dramatically splayed apart in the X-ray structure. Cysteine crosslinking was used to constrain these membrane domains and to show that this large-scale splaying was not necessary for transport activity. Furthermore, dimer stability was not compromised by mutagenesis of elements in the cytoplasmic domain, suggesting that the extensive interface between membrane domains is a strong determinant of dimerization. As with other secondary transporters, this interface could provide a stable scaffold for movements of the four-helix bundle that confers alternating access of these ions to opposite sides of the membrane.