6OFR

The crystal structure of the outer membrane transporter YddB from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Literature

Protease-associated import systems are widespread in Gram-negative bacteria.

Grinter, R.Leung, P.M.Wijeyewickrema, L.C.Littler, D.Beckham, S.Pike, R.N.Walker, D.Greening, C.Lithgow, T.

(2019) PLoS Genet 15: e1008435-e1008435

  • DOI: https://doi.org/10.1371/journal.pgen.1008435
  • Primary Citation of Related Structures:  
    6OFR, 6OFS, 6OFT

  • PubMed Abstract: 

    Bacteria have evolved sophisticated uptake machineries in order to obtain the nutrients required for growth. Gram-negative plant pathogens of the genus Pectobacterium obtain iron from the protein ferredoxin, which is produced by their plant hosts. This iron-piracy is mediated by the ferredoxin uptake system (Fus), a gene cluster encoding proteins that transport ferredoxin into the bacterial cell and process it proteolytically. In this work we show that gene clusters related to the Fus are widespread in bacterial species. Through structural and biochemical characterisation of the distantly related Fus homologues YddB and PqqL from Escherichia coli, we show that these proteins are analogous to components of the Fus from Pectobacterium. The membrane protein YddB shares common structural features with the outer membrane ferredoxin transporter FusA, including a large extracellular substrate binding site. PqqL is an active protease with an analogous periplasmic localisation and iron-dependent expression to the ferredoxin processing protease FusC. Structural analysis demonstrates that PqqL and FusC share specific features that distinguish them from other members of the M16 protease family. Taken together, these data provide evidence that protease associated import systems analogous to the Fus are widespread in Gram-negative bacteria.


  • Organizational Affiliation

    School of Biological Sciences, Monash University, Clayton, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TonB-dependent outer membrane receptor762Escherichia coliMutation(s): 0 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for P31827 (Escherichia coli (strain K12))
Explore P31827 
Go to UniProtKB:  P31827
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31827
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.52α = 90
b = 76.52β = 90
c = 412.75γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2019-10-02 
  • Deposition Author(s): Grinter, R.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106077/Z/14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary