1GDU

FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION

Summary for 1GDU

• Entry DOI: 10.2210/pdb1gdu/pdb
• Related: 1fn8 1fy4 1fy5 1gdn 1gdq 1try
• Descriptor: TRYPSIN, GLY-ALA-ARG, SULFATE ION, ... (4 entities in total)
• Functional Keywords: beta-barrel, hydrolase
• Biological source: Fusarium oxysporum
• Cellular location: Secreted: P35049
• Total number of polymer chains: 2
• Total formula weight: 22599.89

Authors

Rypniewski, W.R.,Oestergaard, P.,Noerregaard-Madsen, M.,Dauter, M.,Wilson, K.S. (deposition date: 2000-09-29, release date: 2001-02-07, Last modification date: 2024-10-30)

Primary citation

Rypniewski, W.R.,Ostergaard, P.R.,Norregaard-Madsen, M.,Dauter, M.,Wilson, K.S.
Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.
Acta Crystallogr.,Sect.D, 57:8-19, 2001

PubMed Abstract: 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.

PubMed: 11134922
DOI: 10.1107/S0907444900014116

Experimental method

X-RAY DIFFRACTION (1.07 Å)