3H90

Structural basis for the autoregulation of the zinc transporter YiiP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural basis for autoregulation of the zinc transporter YiiP.

Lu, M., Chai, J., Fu, D.

(2009) Nat.Struct.Mol.Biol. 16: 1063-1067

  • DOI: 10.1038/nsmb.1662

  • PubMed Abstract: 

    • Zinc transporters have crucial roles in cellular zinc homeostatic control. The 2.9-A resolution structure of the zinc transporter YiiP from Escherichia coli reveals a richly charged dimer interface stabilized by zinc binding. Site-directed fluorescen ...

    Zinc transporters have crucial roles in cellular zinc homeostatic control. The 2.9-A resolution structure of the zinc transporter YiiP from Escherichia coli reveals a richly charged dimer interface stabilized by zinc binding. Site-directed fluorescence resonance energy transfer (FRET) measurements and mutation-activity analysis suggest that zinc binding triggers hinge movements of two electrically repulsive cytoplasmic domains pivoting around four salt bridges situated at the juncture of the cytoplasmic and transmembrane domains. These highly conserved salt bridges interlock transmembrane helices at the dimer interface, where they are well positioned to transmit zinc-induced interdomain movements to reorient transmembrane helices, thereby modulating coordination geometry of the active site for zinc transport. The cytoplasmic domain of YiiP is a structural mimic of metal-trafficking proteins and the metal-binding domains of metal-transporting P-type ATPases. The use of this common structural module to regulate metal coordination chemistry may enable a tunable transport activity in response to cytoplasmic metal fluctuations.

    Organizational Affiliation: 

    Biology Department, Brookhaven National Laboratory, Upton, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferrous-iron efflux pump fieF
A, B, C, D
283Escherichia coli (strain K12)Gene Names: fieF (yiiP)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Cation Diffusion Facilitator (CDF) Family		Protein: 
YiiP Zinc Transporter
Find proteins for P69380 (Escherichia coli (strain K12))
Go to UniProtKB:  P69380
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG
Download SDF File 
Download CCD File 
A, B, C, D
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 105.657α = 90.00
b = 130.704β = 93.28
c = 115.757γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-04-29 
  • Released Date: 2009-09-08 
  • Deposition Author(s): Lu, M.

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance