3ER5

THE ACTIVE SITE OF ASPARTIC PROTEINASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-ray-crystallographic studies of complexes of pepstatin A and a statine-containing human renin inhibitor with endothiapepsin.

Bailey, D.Cooper, J.B.Veerapandian, B.Blundell, T.L.Atrash, B.Jones, D.M.Szelke, M.

(1993) Biochem.J. 289 ( Pt 2): 363-371

  • DOI: 10.1042/bj2890363

  • PubMed Abstract: 
  • H-189, a synthetic human renin inhibitor, and pepstatin A, a naturally occurring inhibitor of aspartic proteinases, have been co-crystallized with the fungal aspartic proteinase endothiapepsin (EC 3.4.23.6). H-189 [Pro-His-Pro-Phe-His-Sta-(statyl)-Va ...

    H-189, a synthetic human renin inhibitor, and pepstatin A, a naturally occurring inhibitor of aspartic proteinases, have been co-crystallized with the fungal aspartic proteinase endothiapepsin (EC 3.4.23.6). H-189 [Pro-His-Pro-Phe-His-Sta-(statyl)-Val-Ile-His-Lys] is an analogue of human angiotensinogen. Pepstatin A [Iva(isovaleryl)-Val-Val-Sta-Ala-Sta] is a blocked pentapeptide which inhibits many aspartic proteinases. The structures of the complexes have been determined by X-ray diffraction and refined to crystallographic R-factors of 0.15 and 0.16 at resolutions of 0.18 nm (1.8 A) and 0.2 nm (2.0 A) respectively. H-189 is in an extended conformation, in which the statine residue is a dipeptide analogue of P1 and P'1 as indicated by the conformation and network of contacts and hydrogen bonds. Pepstatin A has an extended conformation to the P'2 alanine residue, but the leucyl side chain of the terminal statine residue binds back into the S'1 subsite, and an inverse gamma-turn occurs between P'1 and P'3. The hydroxy moiety of the statine at P1 in both complexes displaces the solvent molecule that hydrogen-bonds with the catalytic aspartate residues (32 and 215) in the native enzyme. Solvent molecules originally present in the native structure at the active site are displaced on inhibitor binding (12 when pepstatin A binds; 16 when H-189 binds).


    Related Citations: 
    • 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
    • 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
    • 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
    • Four-Fold Structural Repeat in the Acid Proteases
      Blundell, T.L.,Sewell, B.T.,Mclachlan, A.D.
      (1979) Biochim.Biophys.Acta 580: 24
    • 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 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


    Organizational Affiliation

    Department of Crystallography, Birkbeck College, University of London, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDOTHIAPEPSIN
E
330Cryphonectria parasiticaMutation(s): 0 
Gene Names: EAPA (EPN-1)
EC: 3.4.23.22
Find proteins for P11838 (Cryphonectria parasitica)
Go to UniProtKB:  P11838
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H-189
I
10Bos taurusMutation(s): 0 
Gene Names: AGT (SERPINA8)
Find proteins for P01017 (Bos taurus)
Go to Gene View: AGT
Go to UniProtKB:  P01017
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000430
Query on PRD_000430
IH 189Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.100α = 90.00
b = 75.400β = 97.00
c = 42.800γ = 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: 1991-04-15
    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