4APE

THE ACTIVE SITE OF ASPARTIC PROTEINASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Active Site of Aspartic Proteinases

Pearl, L.Blundell, T.

(1984) FEBS Lett. 174: 96-101

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The active site of the aspartic proteinase, endothiapepsin, has been defined by X-ray analysis and restrained least-squares refinement at 2.1 A resolution with a crystallographic agreement value of 0.16. The environments of the two catalytically impo ...

    The active site of the aspartic proteinase, endothiapepsin, has been defined by X-ray analysis and restrained least-squares refinement at 2.1 A resolution with a crystallographic agreement value of 0.16. The environments of the two catalytically important aspartyl groups are remarkably similar and the contributions of the NH2- and COOH-terminal domains to the catalytic centre are related by a local 2-fold axis. The carboxylates of the aspartyls share a hydrogen bond and have equivalent contacts to a bound water molecule or hydroxonium ion lying on the local diad. The main chains around 32 and 215 are connected by a novel interaction involving diad-related threonines. It is suggested that the two pKa values of the active site aspartyls arise from a structure not unlike that in maleic acid with a hydrogen-bonded intermediate species and a dicarboxylate characterised by electrostatic repulsions between the two negatively charged groups.


    Related Citations: 
    • X-Ray Analysis and Circular Dichroism of the Acid Protease from Endothia Parasitica and Chymosin
      Jenkins, J.,Tickle, I.,Sewell, T.,Ungaretti, L.,Wollmer, A.,Blundell, T.
      (1977) Adv.Exp.Med.Biol. 95: 43
    • 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
    • Active Site of Acid Proteinases
      Blundell, T.L.,Jones, H.B.,Khan, G.,Taylor, G.,Sewell, T.S.,Pearl, L.H.,Wood, S.P.
      (1979) Proc.FEBS Meet. 60: 281
    • Structural Evidence for Gene Duplication in the Evolution of Acid Proteases
      Tang, J.,James, M.N.G.,Hsu, I.N.,Jenkins, J.A.,Blundell, T.L.
      (1978) Nature 271: 618
    • Four-Fold Structural Repeat in the Acid Proteases
      Blundell, T.L.,Sewell, B.T.,Mclachlan, A.D.
      (1979) Biochim.Biophys.Acta 580: 24
    • The Three-Dimensional Structure of Acid Proteinases
      Blundell, T.L.,Jenkins, J.A.,Khan, G.,Roychowdhury, P.,Sewell, T.,Tickle, I.J.,Wood, E.A.
      (1979) Proc.FEBS Meet. 52: 81



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDOTHIAPEPSIN
A
330Cryphonectria parasiticaMutation(s): 0 
Gene Names: EAPA (EPN-1)
EC: 3.4.23.22
Find proteins for P11838 (Cryphonectria parasitica)
Go to UniProtKB:  P11838
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.600α = 90.00
b = 74.050β = 110.00
c = 45.700γ = 90.00
Software Package:
Software NamePurpose
RESTRAINrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1986-07-14
    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