2PV3

Crystallographic Structure of SurA fragment lacking the second peptidyl-prolyl isomerase domain complexed with peptide NFTLKFWDIFRK

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.284 

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This is version 1.3 of the entry. See complete history. 


Literature

The Periplasmic Bacterial Molecular Chaperone SurA Adapts its Structure to Bind Peptides in Different Conformations to Assert a Sequence Preference for Aromatic Residues.

Xu, X., Wang, S., Hu, Y.X., McKay, D.B.

(2007) J Mol Biol 373: 367-381

  • DOI: 10.1016/j.jmb.2007.07.069
  • Primary Citation of Related Structures:  
    2PV1, 2PV2, 2PV3

  • PubMed Abstract: 

    • The periplasmic molecular chaperone protein SurA facilitates correct folding and maturation of outer membrane proteins in Gram-negative bacteria. It preferentially binds peptides that have a high fraction of aromatic amino acids. Phage display selections, isothermal titration calorimetry and crystallographic structure determination have been used to elucidate the basis of the binding specificity ...

    The periplasmic molecular chaperone protein SurA facilitates correct folding and maturation of outer membrane proteins in Gram-negative bacteria. It preferentially binds peptides that have a high fraction of aromatic amino acids. Phage display selections, isothermal titration calorimetry and crystallographic structure determination have been used to elucidate the basis of the binding specificity. The peptide recognition is imparted by the first peptidyl-prolyl isomerase (PPIase) domain of SurA. Crystal structures of complexes between peptides of sequence WEYIPNV and NFTLKFWDIFRK with the first PPIase domain of the Escherichia coli SurA protein at 1.3 A resolution, and of a complex between the dodecapeptide and a SurA fragment lacking the second PPIase domain at 3.4 A resolution, have been solved. SurA binds as a monomer to the heptapeptide in an extended conformation. It binds as a dimer to the dodecapeptide in an alpha-helical conformation, predicated on a substantial structural rearrangement of the SurA protein. In both cases, side-chains of aromatic residues of the peptides contribute a large fraction of the binding interactions. SurA therefore asserts a recognition preference for aromatic amino acids in a variety of sequence configurations by adopting alternative tertiary and quaternary structures to bind peptides in different conformations.

    Related Citations: 
    • Crystallographic structure of SurA, a molecular chaperone that facilitates folding of outer membrane porins
      Bitto, E., McKay, D.B.
      (2002) Structure 10: 1489
    Organizational Affiliation: 

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chaperone surAA, B299Escherichia coliMutation(s): 0 
Gene Names: surA
EC: 5.2.1.8
UniProt
Find proteins for P0ABZ6 (Escherichia coli (strain K12))
Explore P0ABZ6 
Go to UniProtKB:  P0ABZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABZ6
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
C-peptideC12N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.284 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.33α = 90
b = 148.33β = 90
c = 188.68γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata scaling
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-05-09 
  • Released Date: 2007-10-02 
    • Deposition Author(s): Xu, X., McKay, D.B.

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2017-10-18
    Changes: Refinement description