PDBsum entry 1fni

Hydrolase

PDB id: 1fni

Contents

Protein chain

223 a.a. *

Ligands

SO4

EDO ×4

Metals

_CA

Waters ×158

* Residue conservation analysis

PDB id:

1fni

Name:

Hydrolase

Title:

Crystal structure of porcine beta trypsin with 0.01% polydocanol

Structure:

Trypsin. Chain: a. Ec: 3.4.21.4

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas

Resolution:

1.60Å R-factor: 0.183 R-free: 0.233

Authors:

S.Deepthi,A.Johnson,V.Pattabhi

Key ref:

S.Deepthi et al. (2001). Structures of porcine beta-trypsin-detergent complexes: the stabilization of proteins through hydrophilic binding of polydocanol. Acta Crystallogr D Biol Crystallogr, 57, 1506-1512. PubMed id: 11679713 DOI: 10.1107/S0907444901011143

Date:

22-Aug-00 Release date: 13-Sep-00

Protein chain

P00761  (TRYP_PIG) -  Trypsin from Sus scrofa

Seq: 231 a.a.

Struc: 223 a.a.*

* PDB and UniProt seqs differ at 2 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/S0907444901011143

Acta Crystallogr D Biol Crystallogr 57:1506-1512 (2001)

PubMed id: 11679713

Structures of porcine beta-trypsin-detergent complexes: the stabilization of proteins through hydrophilic binding of polydocanol.

S.Deepthi, A.Johnson, V.Pattabhi.

ABSTRACT

Polydocanol has a wide range of medical applications, especially in sclerotherapy of many diseases such as gastrointestinal antiplastia, oesophageal haemangioma etc. It is of interest to study the mode of binding of this medically important detergent and its subsequent action on proteins. Here, three crystal structures of serine protease trypsin are reported in the presence of varying concentrations of polydocanol in order to elucidate its mode of binding and interactions with proteins. Polydocanol binds to the protein with its hydrophilic head rather than the hydrophobic tail as is the case with other detergents such as SDS and MEGA-8. This hydrophilic binding mode results in the binding sites of polydocanol being distributed on the surface of the enzyme. There are at least 11 binding sites for polydocanol in trypsin. Polydocanol forms part of the large-scale water networks which connect distant regions of the enzyme, thereby stabilizing it. The hydrophilic binding of polydocanol also results in cross-linked pairs of trypsin molecules.

Selected figure(s)

Figure 1.
Figure 1 2F[o] - F[c] (darker lines) with 1 and F[o] - F[c] (lighter lines) with 2 level omit maps (residues 29-56 are omitted) showing GYC density and GYC-mediated intermolecular interactions of the protein.

Figure 4.
Figure 4 2F[o] - F[c] map showing electron density for a sulfate molecule at the active site. Hydrogen bonds with His57, Ser195 and Gly193 are also shown.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1506-1512) copyright 2001.

Figures were selected by an automated process.