1fy4: Difference between revisions

Revision as of 16:53, 2 May 2008

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. 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 Page seeded by OCA on Fri May 2 16:53:46 2008

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OCA

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 [[Image:1fy4.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 1fy4 |SIZE=350|CAPTION= <scene name='initialview01'>1fy4</scene>, resolution 0.81&Aring;
+The line below this paragraph, containing "STRUCTURE_1fy4", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1fy4|  PDB=1fy4  |  SCENE=  }}
-|RELATEDENTRY=[[1try|1try]], [[1fn8|1fn8]], [[1gdn|1gdn]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fy4 OCA], [http://www.ebi.ac.uk/pdbsum/1fy4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fy4 RCSB]</span>
-}}
 '''FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION'''
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 [[Category: Rypniewski, W R.]]
 [[Category: Wilson, K S.]]
-[[Category: beta barrel]]
+[[Category: Beta barrel]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 16:53:46 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:32:31 2008''