2QA9

Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

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This is version 1.1 of the entry. See complete history


Literature

1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB).

Lee, T.W.James, M.N.

(2008) Biochim Biophys Acta 1784: 319-334

  • DOI: 10.1016/j.bbapap.2007.11.012
  • Primary Citation of Related Structures:  
    2QA9, 2QAA

  • PubMed Abstract: 
  • Streptogrisin B (SGPB) has served as one of the models for studying the catalytic activities of serine peptidases. Here we report its native crystal structures at pH 4.2 at a resolution of 1.18A, and at pH 7.3 at a resolution of 1.23A. Unexpectedly, outstanding electron density peaks occurred in the active site and the substrate-binding region of SGPB in the computed maps at both pHs ...

    Streptogrisin B (SGPB) has served as one of the models for studying the catalytic activities of serine peptidases. Here we report its native crystal structures at pH 4.2 at a resolution of 1.18A, and at pH 7.3 at a resolution of 1.23A. Unexpectedly, outstanding electron density peaks occurred in the active site and the substrate-binding region of SGPB in the computed maps at both pHs. The densities at pH 4.2 were assigned as a tetrapeptide, Asp-Ala-Ile-Tyr, whereas those at pH 7.3 were assigned as a tyrosine molecule and a leucine molecule existing at equal occupancies in both of the SGPB molecules in the asymmetric unit. Refinement with relaxed geometric restraints resulted in molecular structures representing mixtures of the second tetrahedral intermediates and the enzyme-product complexes of SGPB existing in a pH-dependent equilibrium. Structural comparisons with the complexes of SGPB with turkey ovomucoid third domain (OMTKY3) and its variants have shown that, upon the formation of the tetrahedral intermediate, residues Glu192A to Gly193 of SGPB move towards the alpha-carboxylate O of residue P1 of the bound species, and adjustments in the side-chain conformational angles of His57 and Ser195 of SGPB favor the progression of the catalytic mechanism of SGPB.


    Organizational Affiliation

    Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Room 4-29, Medical Sciences Building, Edmonton, Alberta T6G 2H7, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Streptogrisin-BA [auth E]185Streptomyces griseusMutation(s): 0 
Gene Names: sprB
EC: 3.4.21.81
Find proteins for P00777 (Streptomyces griseus)
Explore P00777 
Go to UniProtKB:  P00777
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
4-mer peptide DAIYB [auth I]4Streptomyces griseusMutation(s): 0 
Gene Names: sprB
EC: 3.4.21.81
Find proteins for P00777 (Streptomyces griseus)
Explore P00777 
Go to UniProtKB:  P00777
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.461α = 90
b = 107.47β = 90
c = 36.792γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance