3APR

BINDING OF A REDUCED PEPTIDE INHIBITOR TO THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS. IMPLICATIONS FOR A MECHANISM OF ACTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action.

Suguna, K.Padlan, E.A.Smith, C.W.Carlson, W.D.Davies, D.R.

(1987) Proc.Natl.Acad.Sci.USA 84: 7009-7013


  • PubMed Abstract: 
  • A peptide inhibitor, having the sequence D-His-Pro-Phe-His-Phe psi [CH2-NH]Phe-Val-Tyr, with a reduced bond between the two adjacent phenylalanines, has been diffused into crystals of the aspartic proteinase from Rhizopus chinensis (rhizopuspepsin, E ...

    A peptide inhibitor, having the sequence D-His-Pro-Phe-His-Phe psi [CH2-NH]Phe-Val-Tyr, with a reduced bond between the two adjacent phenylalanines, has been diffused into crystals of the aspartic proteinase from Rhizopus chinensis (rhizopuspepsin, EC 3.4.23.6). X-ray diffraction data to 1.8-A resolution have been collected on the complex, which has been subjected to restrained least-squares refinement to an R-factor (R equals the sum of the absolute value of the difference between the observed and calculated structure factor amplitudes divided by the sum of the observed structure factor amplitudes) of 14.7%. The inhibitor lies within the major groove of the enzyme and is clearly defined with the exception of the amino-terminal D-histidine and the carboxyl-terminal tyrosine. The reduced peptide bond is located in the active site with close contacts to the two catalytic aspartyl groups. The active-site water molecule that is held between the two carboxyl groups is displaced by the inhibitor, as are a number of other water molecules seen in the binding groove of the native enzyme. A mechanism of action for this class of enzymes is proposed from these results.


    Related Citations: 
    • Structure and Refinement at 1.8 Angstroms Resolution of the Aspartic Proteinase from Rhizopus Chinensis
      Suguna, K.,Bott, R.R.,Padlan, E.A.,Subramanian, E.,Sheriff, S.,Cohen, G.H.,Davies, D.R.
      (1987) J.Mol.Biol. 196: 877
    • Three-Dimensional Structure of the Complex of the Rhizopus Chinensis Carboxyl Proteinase and Pepstatin at 2.5 Angstroms Resolution
      Bott, R.R.,Subramanian, E.,Davies, D.R.
      (1982) Biochemistry 21: 6956
    • Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica
      Subramanian, E.,Swan, I.D.A.,Liu, M.,Davies, D.R.,Jenkins, J.A.,Tickle, I.J.,Blundell, T.L.
      (1977) Proc.Natl.Acad.Sci.USA 74: 556
    • The Crystal Structure of an Acid Protease from Rhizopus Chinensis at 2.5 Angstroms Resolution
      Subramanian, E.,Liu, M.,Swan, I.D.A.,Davies, D.R.
      (1977) Adv.Exp.Med.Biol. 95: 33


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RHIZOPUSPEPSIN
E
325Rhizopus chinensisMutation(s): 0 
EC: 3.4.23.21
Find proteins for P06026 (Rhizopus chinensis)
Go to UniProtKB:  P06026
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REDUCED PEPTIDE INHIBITOR
I
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.370α = 90.00
b = 60.610β = 90.00
c = 106.770γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1988-01-16
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other