2spz
From Proteopedia
(New page: 200px<br /><applet load="2spz" size="450" color="white" frame="true" align="right" spinBox="true" caption="2spz" /> '''STAPHYLOCOCCAL PROTEIN A, Z-DOMAIN, NMR, 10 ...) |
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| - | [[Image:2spz.gif|left|200px]]<br /><applet load="2spz" size=" | + | [[Image:2spz.gif|left|200px]]<br /><applet load="2spz" size="350" color="white" frame="true" align="right" spinBox="true" |
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'''STAPHYLOCOCCAL PROTEIN A, Z-DOMAIN, NMR, 10 STRUCTURES'''<br /> | '''STAPHYLOCOCCAL PROTEIN A, Z-DOMAIN, NMR, 10 STRUCTURES'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Staphylococcal protein A (SpA) is a cell-wall-bound pathogenicity factor | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 2SPZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure | + | 2SPZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry 1SPZ. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SPZ OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Staphylococcus aureus]] | [[Category: Staphylococcus aureus]] | ||
| - | [[Category: Lyons, B | + | [[Category: Lyons, B A.]] |
| - | [[Category: Montelione, G | + | [[Category: Montelione, G T.]] |
[[Category: Tashiro, M.]] | [[Category: Tashiro, M.]] | ||
[[Category: Tejero, R.]] | [[Category: Tejero, R.]] | ||
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[[Category: three-helical bundle structure]] | [[Category: three-helical bundle structure]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:49:24 2008'' |
Revision as of 16:49, 21 February 2008
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STAPHYLOCOCCAL PROTEIN A, Z-DOMAIN, NMR, 10 STRUCTURES
Overview
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.
About this Structure
2SPZ is a Single protein structure of sequence from Staphylococcus aureus. This structure supersedes the now removed PDB entry 1SPZ. Full crystallographic information is available from OCA.
Reference
High-resolution solution NMR structure of the Z domain of staphylococcal protein A., Tashiro M, Tejero R, Zimmerman DE, Celda B, Nilsson B, Montelione GT, J Mol Biol. 1997 Oct 3;272(4):573-90. PMID:9325113
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