1PEK

STRUCTURE OF THE COMPLEX OF PROTEINASE K WITH A SUBSTRATE-ANALOGUE HEXA-PEPTIDE INHIBITOR AT 2.2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the complex of proteinase K with a substrate analogue hexapeptide inhibitor at 2.2-A resolution.

Betzel, C.Singh, T.P.Visanji, M.Peters, K.Fittkau, S.Saenger, W.Wilson, K.S.

(1993) J.Biol.Chem. 268: 15854-15858


  • PubMed Abstract: 
  • The crystal structure of a transition state/product complex formed by the interaction between proteinase K and the substrate analogue N-Ac-L-Pro-L-Ala-L-Pro-L-Phe-D-Ala-L-Ala-NH2 has been determined at a resolution of 2.2 A and refined to an R-factor ...

    The crystal structure of a transition state/product complex formed by the interaction between proteinase K and the substrate analogue N-Ac-L-Pro-L-Ala-L-Pro-L-Phe-D-Ala-L-Ala-NH2 has been determined at a resolution of 2.2 A and refined to an R-factor of 0.165 for 12,725 reflections. The inhibitor forms a stable complex through a series of hydrogen bonds with protein atoms and water molecules. The inhibitor is hydrolyzed between Phe 4I and D-Ala5I (I indicates inhibitor). The two fragments are separated by a distance of 3.07 A between the carbonyl carbon and the main chain nitrogen. Both fragments remain bound to the protein. The N-terminal fragment occupies subsites S5 to S1, whereas the C-terminal part is bound in S1' and S2', the first time that electron density for a substrate analogue has been observed in the P1' and P2' sites of a subtilisin-like enzyme. The flexible segments of the substrate recognition sites Gly100-Tyr104 and Ser132-Gly136 move appreciably to accommodate the inhibitor. Biochemical results indicate an inhibition by this specifically designed peptide of 95%.


    Related Citations: 
    • Three-Dimensional Structure of Proteinase K at 0.15-Nm Resolution
      Betzel, C.,Pal, G.P.,Saenger, W.
      (1988) Eur.J.Biochem. 178: 155


    Organizational Affiliation

    European Molecular Biology Laboratory, Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEINASE K
E
279Engyodontium albumGene Names: PROK
EC: 3.4.21.64
Find proteins for P06873 (Engyodontium album)
Go to UniProtKB:  P06873
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE PRO-ALA-PRO-PHE
C
4N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
D-DAL-ALA-NH2
D
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
D
NON-POLYMERH2 N

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DAL
Query on DAL
D
D-PEPTIDE LINKINGC3 H7 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.280α = 90.00
b = 68.280β = 90.00
c = 107.870γ = 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: 1994-01-31
    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: 2017-11-29
    Type: Advisory, Derived calculations, Other