1GBB

Alpha-lytic protease with met 190 replaced by ALA AND GLY 216 replaced by ALA complex with METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Work: 0.142 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity.

Mace, J.E.Agard, D.A.

(1995) J Mol Biol 254: 720-736

  • DOI: 10.1006/jmbi.1995.0650
  • Primary Citation of Related Structures:  
    1GBC, 1GBB, 1GBA, 1GBK, 1GBJ, 1GBI, 1GBH, 1GBF, 1GBE, 1GBD

  • PubMed Abstract: 
  • Gly216 in the active site of the broadly specific MA190 mutant of alpha-lytic protease has been found to be remarkably tolerant of amino acid substitutions. Side-chains as large as Trp can be accommodated within the substrate-binding pocket without a ...

    Gly216 in the active site of the broadly specific MA190 mutant of alpha-lytic protease has been found to be remarkably tolerant of amino acid substitutions. Side-chains as large as Trp can be accommodated within the substrate-binding pocket without abolishing catalysis, and have major effects upon the substrate specificity of the enzyme. Kinetic characterization of eleven enzymatically active mutants against a panel of eight substrates clearly revealed the functional consequences of the substitutions at position 216. To understand better the structural basis for their altered specificity, the GA216 + MA190 and GL216 + MA190 mutants have been crystallized both with and without a representative series of peptide boronic acid transition-state analog inhibitors. An empirical description and non-parametric statistical analysis of structural variation among these enzyme: inhibitor complexes is presented. The roles of active site plasticity and dynamics in alpha-lytic protease function and substrate preference are also addressed. The results strongly suggest that substrate specificity determination in alpha-lytic protease is a distributed property of the active site and substrate molecule.


    Related Citations: 
    • Structural Basis for Broad Specificity in Alpha-Lytic Protease
      Bone, R., Fujushige, A., Kettner, C.A., Agard, D.A.
      (1991) Biochemistry 30: 10388
    • Structural Plasticity Broadens the Specificity of an Engineered Protease
      Bone, R., Silen, J.L., Agard, D.A.
      (1989) Nature 339: 191
    • Structural Analysis of Specificity: Alpha-Lytic Protease Complexes with Analogues of Reaction Intermediates
      Bone, R., Frank, D., Kettner, D., Agard, D.A.
      (1989) Biochemistry 28: 7600
    • 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 27: 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

    Howard Hughes Medical Institute, University of California, San Francisco 94143-0448, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-LYTIC PROTEASEA198Lysobacter enzymogenesMutation(s): 2 
Gene Names: ALPHA-LYTIC PROTEASE PREPROENZalpha-LP
EC: 3.4.21.12
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-ALANINE BORONIC ACID INHIBITORP5N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
B2A
Query on B2A
PPEPTIDE-LIKEC2 H8 B N O2ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000314
Query on PRD_000314
PMETHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACIDPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Work: 0.142 
  • R-Value Observed: 0.142 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.2α = 90
b = 66.2β = 90
c = 80.09γ = 120
Software Package:
Software NamePurpose
RIGAKUdata collection
X-PLORmodel building
X-PLORrefinement
RIGAKUdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-29
    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