1Y3D

Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 R67A mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2

Radisky, E.S., Lu, C.J., Kwan, G., Koshland Jr., D.E.

(2005) Biochemistry 44: 6823-6830

  • DOI: 10.1021/bi047301w
  • Primary Citation of Related Structures:  
    1Y1K, 1Y33, 1Y34, 1Y3B, 1Y3C, 1Y3D, 1Y3F, 1Y48, 1Y4A, 1Y4D

  • PubMed Abstract: 

    • A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues involved in intramolecular interactions that shape and constrain the binding loop, were studied to determine their relative importance for inhibition of the serine protease subtilisin BPN', and for resistance of the inhibitor to proteolysis ...

    A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues involved in intramolecular interactions that shape and constrain the binding loop, were studied to determine their relative importance for inhibition of the serine protease subtilisin BPN', and for resistance of the inhibitor to proteolysis. These functional properties were investigated in tandem with the crystal structures of the mutant inhibitor-enzyme complexes. A dense hydrogen bonding network that supports the binding loop in the vicinity of the scissile bond was found to be important both for enzyme affinity and for stability to proteolysis. Structural analysis, in combination with biochemical measurements, allows differentiation of the structural components most important for resistance to proteolysis and/or binding. The most critical participating residues in the network were found to be Thr-58, Glu-60, Arg-65, and Gly-83. Glu-60 is more important for resistance to proteolysis than for binding, while Arg-65 and two other Arg residues play a greater role in binding than in resistance to proteolysis. Structural comparisons reveal a wide variety of subtle conformational changes in response to mutation, with built-in robustness in the hydrogen bond network, such that loss of one contact is compensated by other new contacts.

    Organizational Affiliation: 

    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
subtilisin BPN'A [auth E]281Bacillus amyloliquefaciensMutation(s): 0 
Gene Names: apr
EC: 3.4.21.62
UniProt
Find proteins for P00782 (Bacillus amyloliquefaciens)
Explore P00782 
Go to UniProtKB:  P00782
Entity Groups  
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UniProt GroupP00782
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
chymotrypsin inhibitor 2B [auth I]64Hordeum vulgareMutation(s): 1 
Gene Names: Ica-2
UniProt
Find proteins for Q40059 (Hordeum vulgare)
Explore Q40059 
Go to UniProtKB:  Q40059
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ40059
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.265α = 90
b = 94.265β = 90
c = 185.574γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
EPMRphasing
REFMACrefinement
CCP4data scaling
TRUNCATEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-17
    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 1.4: 2021-10-20
    Changes: Database references, Derived calculations