3P42 | pdb_00003p42

Structure of GfcC (YmcB), protein encoded by the E. coli group 4 capsule operon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3P42

This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of Escherichia coli Group 4 Capsule Protein GfcC Reveals a Domain Organization Resembling That of Wza.

Sathiyamoorthy, K.Mills, E.Franzmann, T.M.Rosenshine, I.Saper, M.A.

(2011) Biochemistry 50: 5465-5476

  • DOI: https://doi.org/10.1021/bi101869h
  • Primary Citation Related Structures: 
    3P42

  • PubMed Abstract: 

    We report the 1.9 Å resolution crystal structure of enteropathogenic Escherichia coli GfcC, a periplasmic protein encoded by the gfc operon, which is essential for assembly of group 4 polysaccharide capsule (O-antigen capsule). Presumed gene orthologs of gfcC are present in capsule-encoding regions of at least 29 genera of Gram-negative bacteria. GfcC, a member of the DUF1017 family, is comprised of tandem β-grasp (ubiquitin-like) domains (D2 and D3) and a carboxyl-terminal amphipathic helix, a domain arrangement reminiscent of that of Wza that forms an exit pore for group 1 capsule export. Unlike the membrane-spanning C-terminal helix from Wza, the GfcC C-terminal helix packs against D3. Previously unobserved in a β-grasp domain structure is a 48-residue helical hairpin insert in D2 that binds to D3, constraining its position and sequestering the carboxyl-terminal amphipathic helix. A centrally located and invariant Arg115 not only is essential for proper localization but also forms one of two mostly conserved pockets. Finally, we draw analogies between a GfcC protein fused to an outer membrane β-barrel pore in some species and fusion proteins necessary for secreting biofilm-forming exopolysaccharides.


  • Organizational Affiliation
    • Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, USA.

Macromolecule Content 

  • Total Structure Weight: 105.35 kDa 
  • Atom Count: 7,834 
  • Modeled Residue Count: 914 
  • Deposited Residue Count: 944 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Predicted protein
A, B, C, D
236Escherichia coli O127:H6 str. E2348/69Mutation(s): 0 
Gene Names: E2348C_0970E2348_C_0970gfcC
UniProt
Find proteins for B7UN63 (Escherichia coli O127:H6 (strain E2348/69 / EPEC))
Explore B7UN63 
Go to UniProtKB:  B7UN63
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7UN63
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.831α = 90
b = 99.98β = 91.74
c = 69.02γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary