6OFS

The crystal structure of the periplasmic protease PqqL from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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
Probable zinc protease PqqL913Escherichia coli K-12Mutation(s): 0 
Gene Names: pqqLyddCb1494JW1489
EC: 3.4.24
UniProt
Find proteins for P31828 (Escherichia coli (strain K12))
Explore P31828 
Go to UniProtKB:  P31828
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31828
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.674α = 90
b = 98.674β = 90
c = 230.814γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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: 2024-03-13
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description