1fy4: Difference between revisions
New page: left|200px<br /><applet load="1fy4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fy4, resolution 0.81Å" /> '''FUSARIUM OXYSPORUM T... |
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[[Image:1fy4.jpg|left|200px]]<br /><applet load="1fy4" size=" | [[Image:1fy4.jpg|left|200px]]<br /><applet load="1fy4" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1fy4, resolution 0.81Å" /> | caption="1fy4, resolution 0.81Å" /> | ||
'''FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION'''<br /> | '''FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
The X-ray structure of F. oxysporum trypsin has been determined at atomic | The X-ray structure of F. oxysporum trypsin has been determined at atomic resolution, revealing electron density in the binding site which was interpreted as a peptide bound in the sites S1, S2 and S3. The structure, which was initially determined at 1.07 A resolution and 283 K, has an Arg in the S1 specificity pocket. The study was extended to 0.81 A resolution at 100 K using crystals soaked in Arg, Lys and Gln to study in greater detail the binding at the S1 site. The electron density in the binding site was compared between the different structures and analysed in terms of partially occupied and overlapping components of peptide, solvent water and possibly other chemical moieties. Arg-soaked crystals reveal a density more detailed but similar to the original structure, with the Arg side chain visible in the S1 pocket and residual peptide density in the S2 and S3 sites. The density in the active site is complex and not fully interpreted. Lys at high concentrations displaces Arg in the S1 pocket, while some main-chain density remains in sites S2 and S3. Gln has been shown not to bind. The free peptide in the S1-S3 sites binds in a similar way to the binding loop of BPTI or the inhibitory domain of the Alzheimer's beta-protein precursor, with some differences in the S1 site. | ||
==About this Structure== | ==About this Structure== | ||
1FY4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum] with SO4 and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] Full crystallographic information is available from [http:// | 1FY4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FY4 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Noerregaard-Madsen, M.]] | [[Category: Noerregaard-Madsen, M.]] | ||
[[Category: Oestergaard, P.]] | [[Category: Oestergaard, P.]] | ||
[[Category: Rypniewski, W | [[Category: Rypniewski, W R.]] | ||
[[Category: Wilson, K | [[Category: Wilson, K S.]] | ||
[[Category: GOL]] | [[Category: GOL]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
[[Category: beta barrel]] | [[Category: beta barrel]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:43:54 2008'' | ||
Revision as of 13:43, 21 February 2008
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FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
OverviewOverview
The X-ray structure of F. oxysporum trypsin has been determined at atomic resolution, revealing electron density in the binding site which was interpreted as a peptide bound in the sites S1, S2 and S3. The structure, which was initially determined at 1.07 A resolution and 283 K, has an Arg in the S1 specificity pocket. The study was extended to 0.81 A resolution at 100 K using crystals soaked in Arg, Lys and Gln to study in greater detail the binding at the S1 site. The electron density in the binding site was compared between the different structures and analysed in terms of partially occupied and overlapping components of peptide, solvent water and possibly other chemical moieties. Arg-soaked crystals reveal a density more detailed but similar to the original structure, with the Arg side chain visible in the S1 pocket and residual peptide density in the S2 and S3 sites. The density in the active site is complex and not fully interpreted. Lys at high concentrations displaces Arg in the S1 pocket, while some main-chain density remains in sites S2 and S3. Gln has been shown not to bind. The free peptide in the S1-S3 sites binds in a similar way to the binding loop of BPTI or the inhibitory domain of the Alzheimer's beta-protein precursor, with some differences in the S1 site.
About this StructureAbout this Structure
1FY4 is a Single protein structure of sequence from Fusarium oxysporum with and as ligands. Active as Trypsin, with EC number 3.4.21.4 Full crystallographic information is available from OCA.
ReferenceReference
Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding., Rypniewski WR, Ostergaard PR, Norregaard-Madsen M, Dauter M, Wilson KS, Acta Crystallogr D Biol Crystallogr. 2001 Jan;57(Pt 1):8-19. PMID:11134922
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