2PFE

Crystal Structure of Thermobifida fusca Protease A (TFPA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.436 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mesophile versus Thermophile: Insights Into the Structural Mechanisms of Kinetic Stability

Kelch, B.A.Agard, D.A.

(2007) J.Mol.Biol. 370: 784-795

  • DOI: 10.1016/j.jmb.2007.04.078

  • PubMed Abstract: 
  • Obtaining detailed knowledge of folding intermediate and transition state (TS) structures is critical for understanding protein folding mechanisms. Comparisons between proteins adapted to survive extreme temperatures with their mesophilic homologs ar ...

    Obtaining detailed knowledge of folding intermediate and transition state (TS) structures is critical for understanding protein folding mechanisms. Comparisons between proteins adapted to survive extreme temperatures with their mesophilic homologs are likely to provide valuable information on the interactions relevant to the unfolding transition. For kinetically stable proteins such as alpha-lytic protease (alphaLP) and its family members, their large free energy barrier to unfolding is central to their biological function. To gain new insights into the mechanisms that underlie kinetic stability, we have determined the structure and high temperature unfolding kinetics of a thermophilic homolog, Thermobifida fusca protease A (TFPA). These studies led to the identification of a specific structural element bridging the N and C-terminal domains of the protease (the "domain bridge") proposed to be associated with the enhanced high temperature kinetic stability in TFPA. Mutagenesis experiments exchanging the TFPA domain bridge into alphaLP validate this hypothesis and illustrate key structural details that contribute to TFPA's increased kinetic thermostability. These results lead to an updated model for the unfolding transition state structure for this important class of proteases in which domain bridge undocking and unfolding occurs at or before the TS. The domain bridge appears to be a structural element that can modulate the degree of kinetic stability of the different members of this class of proteases.


    Organizational Affiliation

    Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th St. San Francisco, CA 94158-2517, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alkaline serine protease
A, B
186Thermobifida fusca (strain YX)N/A
Find proteins for Q47SP5 (Thermobifida fusca (strain YX))
Go to UniProtKB:  Q47SP5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AES
Query on AES

Download SDF File 
Download CCD File 
A, B
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
AEBSF
C8 H10 F N O2 S
MGSKVZWGBWPBTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.436 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.959α = 90.00
b = 68.552β = 101.98
c = 40.355γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2012-06-06
    Type: Non-polymer description