3PRK

INHIBITION OF PROTEINASE K BY METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYL KETONE. AN X-RAY STUDY AT 2.2-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Inhibition of proteinase K by methoxysuccinyl-Ala-Ala-Pro-Ala-chloromethyl ketone. An x-ray study at 2.2-A resolution.

Wolf, W.M.Bajorath, J.Muller, A.Raghunathan, S.Singh, T.P.Hinrichs, W.Saenger, W.

(1991) J Biol Chem 266: 17695-17699

  • DOI: 10.2210/pdb3prk/pdb
  • Primary Citation of Related Structures:  
    3PRK

  • PubMed Abstract: 
  • The crystal structure of the transition state analog complex formed covalently between proteinase K and methoxysuccinyl-Ala-Ala-Pro-Ala-chloromethyl ketone was determined by x-ray diffraction methods at a resolution of 2.2 A and refined by constrained least squares to an R factor of 19 ...

    The crystal structure of the transition state analog complex formed covalently between proteinase K and methoxysuccinyl-Ala-Ala-Pro-Ala-chloromethyl ketone was determined by x-ray diffraction methods at a resolution of 2.2 A and refined by constrained least squares to an R factor of 19.8% for the 11864 structure amplitudes greater than 1 sigma F. The chloromethyl ketone group is covalently linked with the active site functional groups His69(N epsilon) and Ser224(O gamma). The former has substituted for chlorine and the latter has attacked the carbon of the ketone group, thereby forming the tetrahedral carbon atom of the transition state analog. The peptide part of the inhibitor is in an extended conformation and fills subsites S1 to S5 of the substrate recognition site. Its backbone hydrogens bond with strands 100-104 and 132-136 of the substrate recognition site as the central strand of a three-stranded antiparallel beta-pleated sheet. This sheet formation is associated with a movement by approximately 1 A of strand 100-104 which is probably associated with the insertion of the bulky proline side chain. The methoxysuccinyl group is stacked on the phenolic side chain of Tyr104 that is a part of the bottom of the recognition site. Biochemical studies show that shorter inhibitors of this type are less effective than the longer one, because there are fewer hydrogen bonding and van der Waals/stacking interactions.


    Related Citations: 
    • Synchrotron X-Ray Data Collection and Restrained Least-Squares Refinement of the Crystal Structure of Proteinase K at 1.5 Angstroms Resolution
      Betzel, C., Pal, G.P., Saenger, W.
      (1988) Acta Crystallogr B 44: 163
    • Crystallization of the Bifunctional Proteinase(Slash)Amylase Inhibitor Pki-3 and of its Complex with Proteinase K
      Pal, G.P., Betzel, C., Jany, K.-D., Saenger, W.
      (1986) FEBS Lett 197: 111
    • Active-Site Geometry of Proteinase K. Crystallographic Study of its Complex with a Dipeptide Chloromethyl Ketone Inhibitor
      Betzel, C., Pal, G.P., Struck, M., Jany, K.-D., Saenger, W.
      (1986) FEBS Lett 197: 105
    • Three-Dimensional Structure of Fungal Proteinase K Reveals Similarity to Bacterial Subtilisin
      Paehler, A., Banerjee, A., Dattagupta, J.K., Fujiwara, T., Lindner, K., Pal, G.P., Suck, D., Weber, G., Saenger, W.
      (1984) EMBO J 3: 1311
    • Crystallization of the Fungal Enzyme Proteinase K and Amino Acid Composition
      Dattagupta, J.K., Fujiwara, T., Grishin, E.V., Lindner, K., Manor, P.C., Pieniazek, N.J., Saenger, W., Suck, D.
      (1975) J Mol Biol 97: 267

    Organizational Affiliation

    Institut für Kristallographie, Freie Universität Berlin, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEINASE KA [auth E]279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYL KETONEB [auth I]6N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth E]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALV
Query on ALV
B [auth I]PEPTIDE-LIKEC3 H9 N O2ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.3α = 90
b = 68.3β = 90
c = 108.4γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other