1BOQ

PRO REGION C-TERMINUS: PROTEASE ACTIVE SITE INTERACTIONS ARE CRITICAL IN CATALYZING THE FOLDING OF ALPHA-LYTIC PROTEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pro region C-terminus:protease active site interactions are critical in catalyzing the folding of alpha-lytic protease.

Peters, R.J.Shiau, A.K.Sohl, J.L.Anderson, D.E.Tang, G.Silen, J.L.Agard, D.A.

(1998) Biochemistry 37: 12058-12067

  • DOI: 10.1021/bi980883v

  • PubMed Abstract: 
  • alpha-Lytic protease is encoded with a large (166 amino acid) N-terminal pro region that is required transiently both in vivo and in vitro for the correct folding of the protease domain [Silen, J. L. , and Agard, D. A. (1989) Nature 341, 462-464; Bak ...

    alpha-Lytic protease is encoded with a large (166 amino acid) N-terminal pro region that is required transiently both in vivo and in vitro for the correct folding of the protease domain [Silen, J. L. , and Agard, D. A. (1989) Nature 341, 462-464; Baker, D., et al. (1992) Nature 356, 263-265]. The pro region also acts as a potent inhibitor of the mature enzyme [Baker, D., et al. (1992) Proteins: Struct.,Funct., Genet. 12, 339-344]. This inhibition is mediated through direct steric occlusion of the active site by the C-terminal residues of the pro region [Sohl, J. L., et al. (1997) Biochemistry 36, 3894-3904]. Through mutagenesis and structure-function analyses we have begun to investigate the mechanism by which the pro region acts as a single turnover catalyst to facilitate folding of the mature protease. Of central interest has been mapping the interface between the pro region and the protease and identifying interactions critical for stabilizing the rate-limiting folding transition state. Progressive C-terminal deletions of the pro region were found to have drastic effects on the rate at which the pro region folds the protease but surprisingly little effect on inhibition of protease activity. The observed kinetic data strongly support a model in which the detailed interactions between the pro region C-terminus and the protease are remarkably similar to those of known substrate/inhibitor complexes. Further, mutation of two protease residues near the active site have significant effects on stabilization of the folding transition state (kcat) or in binding to the folding intermediate (KM). Our results suggest a model for the alpha-lytic protease pro region-mediated folding reaction that may be generally applicable to other pro region-dependent folding reactions.


    Related Citations: 
    • Molecular Structure of the Alpha-Lytic Protease from Myxobacter 495 at 2.8 Angstroms Resolution
      Brayer, G.D.,Delbaere, L.T.,James, M.N.
      (1979) J.Mol.Biol. 131: 743
    • Refined Structure of Alpha-Lytic Protease at 1.7 A Resolution. Analysis of Hydrogen Bonding and Solvent Structure
      Fujinaga, M.,Delbaere, L.T.,Brayer, G.D.,James, M.N.
      (1985) J.Mol.Biol. 184: 479
    • Structural Basis for Broad Specificity in Alpha-Lytic Protease
      Bone, R.,Fujishige, A.,Kettner, C.A.,Agard, D.A.
      (1991) Biochemistry 30: 10388
    • Structural Analysis of Specificity: Alpha-Lytic Protease Complexes with Analogues of Reaction Intermediates
      Bone, R.,Frank, D.,Kettner, C.A.,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 26: 7609
    • Structural Plasticity Broadens the Specificity of an Engineered Protease
      Bone, R.,Silen, J.L.,Agard, D.A.
      (1989) Nature 339: 191


    Organizational Affiliation

    The Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California, San Francisco 94143, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ALPHA-LYTIC PROTEASE)
A
198Lysobacter enzymogenesMutation(s): 1 
Gene Names: alpha-LP
EC: 3.4.21.12
Find proteins for P00778 (Lysobacter enzymogenes)
Go to UniProtKB:  P00778
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.159 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.200α = 90.00
b = 66.200β = 90.00
c = 80.200γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance