1BRC

RELOCATING A NEGATIVE CHARGE IN THE BINDING POCKET OF TRYPSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Relocating a negative charge in the binding pocket of trypsin.

Perona, J.J.Tsu, C.A.McGrath, M.E.Craik, C.S.Fletterick, R.J.

(1993) J.Mol.Biol. 230: 934-949

  • DOI: 10.1006/jmbi.1993.1211
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The functional and structural consequences of altering the position of the negatively charged aspartate residue at the base of the specificity pocket of trypsin have been examined by site-directed mutagenesis, kinetic characterization and crystallogr ...

    The functional and structural consequences of altering the position of the negatively charged aspartate residue at the base of the specificity pocket of trypsin have been examined by site-directed mutagenesis, kinetic characterization and crystallographic analysis. Anionic rat trypsin D189G/G226D exhibits a high level of catalytic activity on activated amide substrates, but its relative preference for lysine versus arginine as the P1 site residue is shifted by 30 to 40-fold in favor of lysine. The crystal structure of this variant has been determined in complexes with BPTI (bovine pancreatic trypsin inhibitor), APPI (amyloid beta-protein precursor inhibitor domain) and benzamidine inhibitors, at resolutions of 2.1 A, 2.5 A and 2.2 A, respectively. Asp226 bridges the base of the specificity pocket with its negative charge partially buried by interactions made with Ser190 and Tyr228. An equal reduction in the affinity of the variant enzyme for Arg and Lys substrates is attributable to a decreased electrostatic interaction of each ligand with the relocated aspartate residue. Comparison of structural and functional parameters with those of wild-type trypsin suggests that direct hydrogen-bonding electrostatic contacts in the S1 site do not significantly improve the free energy of substrate binding relative to indirect water-mediated interactions. The conformation adopted by Asp226, as well as by other adjacent side-chain and backbone groups, depends upon the ligand bound in the primary specificity pocket. This structural flexibility may be of critical importance to the retention of catalytic activity by the variant enzyme.


    Related Citations: 
    • X-Ray Crystal Structure of the Protease Inhibitor Domain of Alzheimer'S Amyloid Beta-Protein Precursor
      Hynes, T.R.,Randal, M.,Kennedy, L.A.,Eigenbrot, C.,Kossiakoff, A.A.
      (1990) Biochemistry 29: 10018
    • Crystal Structures of Rat Anionic Trypsin Complexed with the Protein Inhibitors Appi and Bpti
      Perona, J.J.,Tsu, C.A.,Craik, C.S.,Fletterick, R.J.
      (1993) J.Mol.Biol. 230: 919


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
E
223Rattus norvegicusMutation(s): 0 
Gene Names: Prss2 (Try2)
EC: 3.4.21.4
Find proteins for P00763 (Rattus norvegicus)
Go to UniProtKB:  P00763
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AMYLOID BETA-PROTEIN PRECURSOR INHIBITOR DOMAIN (APPI)
I
56Homo sapiensMutation(s): 0 
Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens)
Go to Gene View: APP
Go to UniProtKB:  P05067
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.168 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.100α = 90.00
b = 93.100β = 90.00
c = 62.500γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other