1BRC

RELOCATING A NEGATIVE CHARGE IN THE BINDING POCKET OF TRYPSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 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:  
    1BRA, 1BRC

  • 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 crystallographic analysis ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRYPSINA [auth E]223Rattus norvegicusMutation(s): 0 
Gene Names: Prss2Try2
EC: 3.4.21.4
UniProt
Find proteins for P00763 (Rattus norvegicus)
Explore P00763 
Go to UniProtKB:  P00763
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AMYLOID BETA-PROTEIN PRECURSOR INHIBITOR DOMAIN (APPI)B [auth I]56N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.1α = 90
b = 93.1β = 90
c = 62.5γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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