2W07

Structural determinants of polymerization reactivity of the P pilus adaptor subunit PapF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

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This is version 1.2 of the entry. See complete history


Literature

Structural Determinants of Polymerization Reactivity of the P Pilus Adaptor Subunit Papf.

Verger, D.Rose, R.J.Paci, E.Costakes, G.Daviter, T.Hultgren, S.Remaut, H.Ashcroft, A.E.Radford, S.E.Waksman, G.

(2008) Structure 16: 1724

  • DOI: 10.1016/j.str.2008.08.012
  • Primary Citation of Related Structures:  
    2W07

  • PubMed Abstract: 
  • P pili are important adhesive fibers involved in kidney infection by uropathogenic Escherichia coli. Pilus subunits are characterized by a large groove resulting from lack of a beta strand. Polymerization of pilus subunits occurs via the donor-strand exchange (DSE) mechanism initiated when the N terminus of an incoming subunit interacts with the P5 region/pocket of the previously assembled subunit groove ...

    P pili are important adhesive fibers involved in kidney infection by uropathogenic Escherichia coli. Pilus subunits are characterized by a large groove resulting from lack of a beta strand. Polymerization of pilus subunits occurs via the donor-strand exchange (DSE) mechanism initiated when the N terminus of an incoming subunit interacts with the P5 region/pocket of the previously assembled subunit groove. Here, we solve the structure of the PapD:PapF complex in order to understand why PapF undergoes slow DSE. The structure reveals that the PapF P5 pocket is partially obstructed. MD simulations show this region of PapF is flexible compared with its equivalent in PapH, a subunit that also has an obstructed P5 pocket and is unable to undergo DSE. Using electrospray-ionization mass spectrometry, we show that mutations in the P5 region result in increased DSE rates. Thus, partial obstruction of the P5 pocket serves as a modulating mechanism of DSE.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, University College London, Birkbeck College, Malet Street, London WC1E 7HX, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHAPERONE PROTEIN PAPDA218Escherichia coli UTI89Mutation(s): 0 
Gene Names: papDUTI89_C4892
UniProt
Find proteins for Q1R2W9 (Escherichia coli (strain UTI89 / UPEC))
Explore Q1R2W9 
Go to UniProtKB:  Q1R2W9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MINOR PILIN SUBUNIT PAPFB148Escherichia coli UTI89Mutation(s): 1 
Gene Names: papFUTI89_C4888
UniProt
Find proteins for Q1R2X3 (Escherichia coli (strain UTI89 / UPEC))
Explore Q1R2X3 
Go to UniProtKB:  Q1R2X3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.42α = 90
b = 65.42β = 90
c = 166.11γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance