Expression, crystallization and three-dimensional structure of the catalytic domain of human plasma kallikrein: Implications for structure-based design of protease inhibitors

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

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Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein.

Tang, J.Yu, C.L.Williams, S.R.Springman, E.Jeffery, D.Sprengeler, P.A.Estevez, A.Sampang, J.Shrader, W.Spencer, J.Young, W.McGrath, M.Katz, B.A.

(2005) J Biol Chem 280: 41077-41089

  • DOI: https://doi.org/10.1074/jbc.M506766200
  • Primary Citation of Related Structures:  
    2ANW, 2ANY

  • PubMed Abstract: 

    Plasma kallikrein is a serine protease that has many important functions, including modulation of blood pressure, complement activation, and mediation and maintenance of inflammatory responses. Although plasma kallikrein has been purified for 40 years, its structure has not been elucidated. In this report, we described two systems (Pichia pastoris and baculovirus/Sf9 cells) for expression of the protease domain of plasma kallikrein, along with the purification and high resolution crystal structures of the two recombinant forms. In the Pichia pastoris system, the protease domain was expressed as a heterogeneously glycosylated zymogen that was activated by limited trypsin digestion and treated with endoglycosidase H deglycosidase to reduce heterogeneity from the glycosylation. The resulting protein was chromatographically resolved into four components, one of which was crystallized. In the baculovirus/Sf9 system, homogeneous, crystallizable, and nonglycosylated protein was expressed after mutagenizing three asparagines (the glycosylation sites) to glutamates. When assayed against the peptide substrates, pefachrome-PK and oxidized insulin B chain, both forms of the protease domain were found to have catalytic activity similar to that of the full-length protein. Crystallization and x-ray crystal structure determination of both forms have yielded the first three-dimensional views of the catalytic domain of plasma kallikrein. The structures, determined at 1.85 A for the endoglycosidase H-deglycosylated protease domain produced from P. pastoris and at 1.40 A for the mutagenically deglycosylated form produced from Sf9 cells, show that the protease domain adopts a typical chymotrypsin-like serine protease conformation. The structural information provides insights into the biochemical and enzymatic properties of plasma kallikrein and paves the way for structure-based design of protease inhibitors that are selective either for or against plasma kallikrein.

  • Organizational Affiliation

    Department of Structural Chemistry, Celera Genomics, South San Francisco, California 94080, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
plasma kallikrein, light chain241Homo sapiensMutation(s): 1 
Gene Names: KLKB1KLK3
UniProt & NIH Common Fund Data Resources
Find proteins for P03952 (Homo sapiens)
Explore P03952 
Go to UniProtKB:  P03952
PHAROS:  P03952
GTEx:  ENSG00000164344 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03952
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BEN

Download Ideal Coordinates CCD File 
C7 H8 N2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.886α = 90
b = 63.19β = 90
c = 50.313γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references
  • Version 2.2: 2023-08-23
    Changes: Data collection, Refinement description