7JQK

Crystal structure of the R64A mutant of Bauhinia Bauhinioides Kallikrein Inhibitor complexed with Human Kallikrein 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI.

Li, M.Srp, J.Mares, M.Wlodawer, A.Gustchina, A.

(2021) Acta Crystallogr D Struct Biol 77: 1084-1098

  • DOI: https://doi.org/10.1107/S2059798321006483
  • Primary Citation of Related Structures:  
    7JQK, 7JQN, 7JQO, 7JQV, 7JR1, 7JR2, 7JRX

  • PubMed Abstract: 

    Structures of BbKI, a recombinant Kunitz-type serine protease inhibitor from Bauhinia bauhinioides, complexed with human kallikrein 4 (KLK4) were determined at medium-to-high resolution in four crystal forms (space groups P3 1 21, P6 5 22, P2 1 and P6 1 ). Although the fold of the protein was virtually identical in all of the crystals, some significant differences were observed in the conformation of Arg64 of BbKI, the residue that occupies the S1 pocket in KLK4. Whereas this residue exhibited two orientations in the highest resolution structure (P3 1 21), making either a canonical trypsin-like interaction with Asp189 of KLK4 or an alternate interaction, only a single alternate orientation was observed in the other three structures. A neighboring disulfide, Cys191-Cys220, was partially or fully broken in all KLK4 structures. Four variants of BbKI in which Arg64 was replaced by Met, Phe, Ala and Asp were expressed and crystallized, and their structures were determined in complex with KLK4. Structures of the Phe and Met variants complexed with bovine trypsin and of the Phe variant complexed with α-chymotrypsin were also determined. Although the inhibitory potency of these variant forms of BbKI was lowered by up to four orders of magnitude, only small changes were seen in the vicinity of the mutated residues. Therefore, a totality of subtle differences in KLK4-BbKI interactions within the fully extended interface in the structures of these variants might be responsible for the observed effect. Screening of the BbKI variants against a panel of serine proteases revealed an altered pattern of inhibitory specificity, which was shifted towards that of chymotrypsin-like proteases for the hydrophobic Phe and Met P1 substitutions. This work reports the first structures of plant Kunitz inhibitors with S1-family serine proteases other than trypsin, as well as new insights into the specificity of inhibition of medically relevant kallikreins.


  • Organizational Affiliation

    Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kallikrein-4A [auth E]223Homo sapiensMutation(s): 1 
Gene Names: KLK4EMSP1PRSS17PSTS
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5K2 (Homo sapiens)
Explore Q9Y5K2 
Go to UniProtKB:  Q9Y5K2
PHAROS:  Q9Y5K2
GTEx:  ENSG00000167749 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5K2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Kunitz-type inihibitorB [auth I]165Bauhinia bauhinioidesMutation(s): 1 
UniProt
Find proteins for P83052 (Bauhinia bauhinioides)
Explore P83052 
Go to UniProtKB:  P83052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83052
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.036α = 90
b = 104.036β = 90
c = 86.801γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Database references