3CFZ | pdb_00003cfz

Crystal structure of M. jannaschii periplasmic binding protein ModA/WtpA with bound tungstate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.200 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.179 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3CFZ

This is version 1.2 of the entry. See complete history

Literature

Distorted octahedral coordination of tungstate in a subfamily of specific binding proteins.

Hollenstein, K.Comellas-Bigler, M.Bevers, L.E.Feiters, M.C.Meyer-Klaucke, W.Hagedoorn, P.L.Locher, K.P.

(2009) J Biol Inorg Chem 14: 663-672

  • DOI: https://doi.org/10.1007/s00775-009-0479-7
  • Primary Citation Related Structures: 
    3CFX, 3CFZ, 3CG1, 3CG3, 3CIJ

  • PubMed Abstract: 

    Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). These substrates are captured by an external, high-affinity binding protein, and delivered to ATP binding cassette transporters, which move them across the cell membrane. We have recently reported a crystal structure of the molybdate/tungstate binding protein ModA/WtpA from Archaeoglobus fulgidus, which revealed an octahedrally coordinated central metal atom. By contrast, the previously determined structures of three bacterial homologs showed tetracoordinate molybdenum and tungsten atoms in their binding pockets. Until then, coordination numbers above four had only been found for molybdenum/tungsten in metalloenzymes where these metal atoms are part of the catalytic cofactors and coordinated by mostly non-oxygen ligands. We now report a high-resolution structure of A. fulgidus ModA/WtpA, as well as crystal structures of four additional homologs, all bound to tungstate. These crystal structures match X-ray absorption spectroscopy measurements from soluble, tungstate-bound protein, and reveal the details of the distorted octahedral coordination. Our results demonstrate that the distorted octahedral geometry is not an exclusive feature of the A. fulgidus protein, and suggest distinct binding modes of the binding proteins from archaea and bacteria.


  • Organizational Affiliation
    • Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 33.81 kDa 
  • Atom Count: 2,664 
  • Modeled Residue Count: 289 
  • Deposited Residue Count: 292 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UPF0100 protein MJ1186292Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: modA
UniProt
Find proteins for Q58586 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58586 
Go to UniProtKB:  Q58586
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58586
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WO4

Query on WO4



Download:Ideal Coordinates CCD File
B [auth A]TUNGSTATE(VI)ION
O4 W
PBYZMCDFOULPGH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.200 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.179 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.88α = 90
b = 89.589β = 90
c = 97.868γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations