1P10

STRUCTURAL PLASTICITY AS A DETERMINANT OF ENZYME SPECIFICITY. CREATING BROADLY SPECIFIC PROTEASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural plasticity broadens the specificity of an engineered protease.

Bone, R.Silen, J.L.Agard, D.A.

(1989) Nature 339: 191-195

  • DOI: 10.1038/339191a0
  • Primary Citation of Related Structures:  
    1P09, 1P10

  • PubMed Abstract: 
  • The substrate specificity of alpha-lytic protease has been changed dramatically, with a concomitant increase in activity, by replacing an active-site Met with Ala. The substrate specificity of both this mutant and another similar mutant are extraordinarily broad ...

    The substrate specificity of alpha-lytic protease has been changed dramatically, with a concomitant increase in activity, by replacing an active-site Met with Ala. The substrate specificity of both this mutant and another similar mutant are extraordinarily broad. X-ray crystallographic analysis shows that structural plasticity, a combination of alternate side-chain conformations and binding-site flexibility, allows both large and small substrates to be well accommodated.


    Related Citations: 
    • Structure Analysis of Specificity. Alpha-Lytic Protease Complexes with Analogues of Reaction Intermediates
      Bone, R., Frank, D., Kettner, C., Agard, D.A.
      () To be published --: --
    • Kinetic Properties of the Binding of Alpha-Lytic Protease to Peptide Boronic Acids
      Kettner, C.A., Bone, R., Agard, D.A., Bachovchin, W.W.
      (1988) Biochemistry 27: 7682
    • Serine Protease Mechanism. Structure of an Inhibitory Complex of Alpha-Lytic Protease and a Tightly Bound Peptide Boronic Acid
      Bone, R., Shenvi, A.B., Kettner, C.A., Agard, D.A.
      (1987) Biochemistry 26: 7609
    • Refined Structure of Alpha-Lytic Protease at 1.7 Angstroms Resolution. Analysis of Hydrogen Bonding and Solvent Structure
      Fujinaga, M., Delbaere, L.T.J., Brayer, G.D., James, M.N.G.
      (1985) J Mol Biol 184: 479
    • Molecular Structure of the Alpha-Lytic Protease from Myxobacter 495 at 2.8 Angstroms Resolution
      Brayer, G.D., Delbaere, L.T.J., James, M.N.G.
      (1979) J Mol Biol 131: 743

    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-LYTIC PROTEASEA198Lysobacter enzymogenesMutation(s): 0 
Gene Names: alpha-LP
EC: 3.4.21.12
UniProt
Find proteins for P00778 (Lysobacter enzymogenes)
Explore P00778 
Go to UniProtKB:  P00778
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID INHIBITORB [auth P]5N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
B2V
Query on B2V
B [auth P]PEPTIDE-LIKEC4 H12 B N O2VAL
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Observed: 0.144 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.3α = 90
b = 66.3β = 90
c = 80.3γ = 120
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 1989-04-24 
  • Released Date: 1990-04-15 
  • Deposition Author(s): Bone, R., Agard, D.A.

Revision History  (Full details and data files)

  • Version 1.0: 1990-04-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    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