1EJA

STRUCTURE OF PORCINE TRYPSIN COMPLEXED WITH BDELLASTASIN, AN ANTISTASIN-TYPE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

L-Isoaspartate 115 of porcine beta-trypsin promotes crystallization of its complex with bdellastasin.

Rester, U.Moser, M.Huber, R.Bode, W.

(2000) Acta Crystallogr.,Sect.D 56: 581-588

  • DOI: 10.1107/s0907444900003048

  • PubMed Abstract: 
  • Bdellastasin is a 59-amino-acid, cysteine-rich, antistasin-type inhibitor of sperm acrosin, plasmin and trypsin, isolated from the medicinal leech Hirudo medicinalis. The complex formed between bdellastasin and porcine beta-trypsin has previously bee ...

    Bdellastasin is a 59-amino-acid, cysteine-rich, antistasin-type inhibitor of sperm acrosin, plasmin and trypsin, isolated from the medicinal leech Hirudo medicinalis. The complex formed between bdellastasin and porcine beta-trypsin has previously been crystallized in the presence of PEG in a tetragonal crystal form of space group P4(3)2(1)2 and has now been found to crystallize under high-salt conditions in the enantiomorphic space group P4(1)2(1)2. These structures have been solved and refined to 2.8 and 2.7 A resolution, respectively. Bdellastasin turns out to have an antistasin-like fold exhibiting a bis-domainal structure. In the second new crystal form, the flexible N-terminal subdomain is rotated with respect to the C--terminal subdomain by about 90 degrees, fitting into a cavity formed by symmetry-related trypsin molecules. The canonical inhibitor-proteinase interaction is restricted to the primary binding loop comprising residues Leu31-Lys36 of bdellastasin. During the refinement, a bound sodium ion occupying the calcium-binding site of the porcine beta-trypsin component was discovered. This sodium ion is coordinated in a tetragonal-pyramidal manner, with the geometry of the enclosing loop slightly changed compared with the loop in the presence of calcium. In the crystal form of space group P4(3)2(1)2, the electron density for residue 115 of porcine beta-trypsin clearly indicates the presence of a beta-isomerized L-aspartic acid, which is placed in spatial proximity to segment Thr144--Gly148 of a symmetry-related trypsin molecule. This is the first structurally observed example of an L-isoaspartate in beta--trypsin originating from Asn. A comparison with other known crystal structures of porcine beta-trypsin-macromolecular inhibitor complexes suggests that the deamidation, isomerization and racemization of Asn115 is the key step in crystallization.


    Related Citations: 
    • Bdellastasin, a serine protease inhibitor of the antistasin family from the medical leech (Hirudo medicinalis) - primary structure, expression in yeast, and characterization of native and recombinant inhibitor.
      Moser, M.,Auerswald, E.,Mentele, R.,Eckerskorn, C.,Fritz, H.,Fink, E.
      (1998) Eur.J.Biochem. 253: 212
    • Structure of the Complex of the Antistasin-type Inhibitor Bdellastasin with Trypsin and Modelling of the Bdellastasin-microplasmin System
      Rester, U.,Bode, W.,Moser, M.,Parry, M.A.,Huber, R.,Auerswald, E.
      (1999) J.Mol.Biol. 293: 93


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
A
223Sus scrofaMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00761 (Sus scrofa)
Go to UniProtKB:  P00761
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BDELLASTASIN
B
59Hirudo medicinalisMutation(s): 0 
Find proteins for P82107 (Hirudo medicinalis)
Go to UniProtKB:  P82107
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.191 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.020α = 90.00
b = 70.020β = 90.00
c = 119.480γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATAdata scaling
ROTAVATAdata reduction
CNSrefinement
AMoREphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description