2SPZ

STAPHYLOCOCCAL PROTEIN A, Z-DOMAIN, NMR, 10 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST CONFORMATIONAL ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution solution NMR structure of the Z domain of staphylococcal protein A.

Tashiro, M.Tejero, R.Zimmerman, D.E.Celda, B.Nilsson, B.Montelione, G.T.

(1997) J.Mol.Biol. 272: 573-590

  • DOI: 10.1006/jmbi.1997.1265

  • PubMed Abstract: 
  • Staphylococcal protein A (SpA) is a cell-wall-bound pathogenicity factor from the bacterium Staphylococcus aureus. Because of their small size and immunoglobulin (IgG)-binding activities, domains of protein A are targets for protein engineering effor ...

    Staphylococcal protein A (SpA) is a cell-wall-bound pathogenicity factor from the bacterium Staphylococcus aureus. Because of their small size and immunoglobulin (IgG)-binding activities, domains of protein A are targets for protein engineering efforts and for the development of computational approaches for de novo protein folding. The NMR solution structure of an engineered IgG-binding domain of SpA, the Z domain (an analog of the B domain of SpA), has been determined by simulated annealing with restrained molecular dynamics on the basis of 671 conformational constraints. The Z domain contains three well-defined alpha-helices corresponding to polypeptide segments Lys7 to Leu17 (helix 1), Glu24 to Asp36 (helix 2), and Ser41 to Ala54 (helix 3). A family of ten conformers representing the solution structure of the Z domain was computed by simulated annealing of restrained molecular dynamics using the program CONGEN. The average of the root-mean-square deviations (r.m. s.d.) of the individual NMR conformers, relative to the mean coordinates, for the backbone atoms N, Calpha and C' of residues Phe5 through Ala56 is 0.69 A; the corresponding backbone r.m.s.d. for the three-helical core is 0.44 A. Helices 1, 2 and 3 are antiparallel in orientation (Omega12=-170(+/-4) degrees , Omega13=+16(+/-3) degrees , Omega23=+173(+/-7) degrees ). A comparison of backbone amide hydrogen/deuterium exchange rates in free and IgG-bound Z domains demonstrates that the amide protons of helices 1, 2 and 3 are protected from rapid exchange in both states, indicating that all three helices are also intact in the IgG-bound state. These solution NMR results differ from the previously determined X-ray structure of the similar SpA B domain in complex with the Fc fragment of a human IgG antibody, where helix 3 is not observed in the electron density map and from the solution NMR structure of the B domain, where helix 3 is observed but helix 1 is tilted by approximately 30 degrees with respect to helices 2 and 3. Hydrogen-bonded N-cap and C-cap formation is observed for all three helices of the Z domain; these capping interactions appear to be highly conserved in the five homologous domains of SpA.


    Related Citations: 
    • An Improved Strategy for Determining Resonance Assignments for Isotopically Enriched Proteins and its Application to an Engineered Domain of Staphylococcal Protein A
      Lyons, B.A.,Tashiro, M.,Cedergren, L.,Nilsson, B.,Montelione, G.T.
      (1993) Biochemistry 32: 7839
    • The Mechanism of Binding Staphylococcal Protein a to Immunoglobin G Does not Involve Helix Unwinding
      Jendeberg, L.,Tashiro, M.,Tejero, R.,Lyons, B.A.,Uhlen, M.,Montelione, G.T.,Nilsson, B.
      (1996) Biochemistry 35: 22
    • Structures of Bacterial Immunoglobulin-Binding Domains and Their Complexes with Immunoglobulin
      Tashiro, M.,Montelione, G.T.
      (1995) Curr.Opin.Struct.Biol. 5: 471


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854-5638, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN G BINDING PROTEIN A
A
58Staphylococcus aureusMutation(s): 2 
Gene Names: spa
Find proteins for P38507 (Staphylococcus aureus)
Go to UniProtKB:  P38507
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST CONFORMATIONAL ENERGY 
  • Olderado: 2SPZ Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance