PDBsum entry 1fn8

Hydrolase/hydrolase substrate

PDB id: 1fn8

Contents

Protein chain

224 a.a. *

Ligands

GLY-ALA-ARG

SO4

GOL ×4

Waters ×401

* Residue conservation analysis

PDB id:

1fn8

Name:

Hydrolase/hydrolase substrate

Title:

Fusarium oxysporum trypsin at atomic resolution

Structure:

Trypsin. Chain: a. Gly-ala-arg. Chain: b. Engineered: yes

Source:

Fusarium oxysporum. Organism_taxid: 5507. Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

0.81Å R-factor: 0.109

Authors:

W.R.Rypniewski,P.Oestergaard,M.Noerregaard-Madsen,M.Dauter,K.S.Wilson

Key ref:

W.R.Rypniewski et al. (2001). Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding. Acta Crystallogr D Biol Crystallogr, 57, 8. PubMed id: 11134922 DOI: 10.1107/S0907444900014116

Date:

21-Aug-00 Release date: 07-Feb-01

Protein chain

P03527  (SIGM3_REOVD) -  Outer capsid protein sigma-3 from Reovirus type 3 (strain Dearing)

Seq: 365 a.a.

Struc: 224 a.a.*

* PDB and UniProt seqs differ at 200 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1107/S0907444900014116

Acta Crystallogr D Biol Crystallogr 57:8 (2001)

PubMed id: 11134922

Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.

W.R.Rypniewski, P.R.Ostergaard, M.Nørregaard-Madsen, M.Dauter, K.S.Wilson.

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.

Selected figure(s)

Figure 3.
Figure 3 Schematic representation of TRY-N. Secondary-structure elements forming the N-terminal domain are marked A1-F1 and the C-terminal domain A2-F2 as defined previously (Rypniewski, Mangani et al., 1995[Rypniewski, W. R., Mangani, S., Bruni, B., Orioli, P. L., Casati, M. & Wilson, K. S. (1995). J. Mol. Biol. 251, 282-296.]). The active site is indicated by the side chains of the `catalytic triad': Ser195, His57 and Asp102. The side chain of Asp189 is also shown at the bottom of the `specificity pocket' defining the tryptic substrate specificity. The peptide bound in sites S1 to S3 is indicated by a ball-and-stick model with dark bonds.

Figure 6.
Figure 6 Ligand binding in TRY-LYS2. (a) `Omit' maps calculated as for Fig. 4-(a), at the same contour levels and with similar colouring scheme. Sites 2004-2006 are not occupied in this structure, as shown by the absence of difference density. There is an indication of a double conformation of the Lys side chain, not modelled because of weak density level for refinement. The water at 2102 has been modelled in two alternative conformations: 2102b is at a bonding distance to Lys N , whilst 2102a is at clashing distance, binding in the absence of the peptide ligand. (b) Geometry of the binding site. The labelling scheme is similar to Fig. 4-(b). Some atoms have been omitted for clarity.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 8-0) copyright 2001.

Figures were selected by an automated process.