3URC

T181G mutant of alpha-Lytic Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Functional modulation of a protein folding landscape via side-chain distortion.

Kelch, B.A.Salimi, N.L.Agard, D.A.

(2012) Proc Natl Acad Sci U S A 109: 9414-9419

  • DOI: 10.1073/pnas.1119274109
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ultrahigh-resolution (< 1.0 Å) structures have revealed unprecedented and unexpected details of molecular geometry, such as the deformation of aromatic rings from planarity. However, the functional utility of such energetically costly strain is unkno ...

    Ultrahigh-resolution (< 1.0 Å) structures have revealed unprecedented and unexpected details of molecular geometry, such as the deformation of aromatic rings from planarity. However, the functional utility of such energetically costly strain is unknown. The 0.83 Å structure of α-lytic protease (αLP) indicated that residues surrounding a conserved Phe side-chain dictate a rotamer which results in a ~6° distortion along the side-chain, estimated to cost 4 kcal/mol. By contrast, in the closely related protease Streptomyces griseus Protease B (SGPB), the equivalent Phe adopts a different rotamer and is undistorted. Here, we report that the αLP Phe side-chain distortion is both functional and conserved in proteases with large pro regions. Sequence analysis of the αLP serine protease family reveals a bifurcation separating those sequences expected to induce distortion and those that would not, which correlates with the extent of kinetic stability. Structural and folding kinetics analyses of family members suggest that distortion of this side-chain plays a role in increasing kinetic stability within the αLP family members that use a large Pro region. Additionally, structural and kinetic folding studies of mutants demonstrate that strain alters the folding free energy landscape by destabilizing the transition state (TS) relative to the native state (N). Although side-chain distortion comes at a cost of foldability, it suppresses the rate of unfolding, thereby enhancing kinetic stability and increasing protein longevity under harsh extracellular conditions. This ability of a structural distortion to enhance function is unlikely to be unique to αLP family members and may be relevant in other proteins exhibiting side-chain distortions.


    Organizational Affiliation

    Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-lytic proteaseA198Lysobacter enzymogenesMutation(s): 1 
Gene Names: alpha-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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.645α = 90
b = 65.645β = 90
c = 79.627γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-07-18
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description