1JCM

TRPC STABILITY MUTANT CONTAINING AN ENGINEERED DISULPHIDE BRIDGE AND IN COMPLEX WITH A CDRP-RELATED SUBSTRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.241 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Stabilization of a (betaalpha)8-barrel protein by an engineered disulfide bridge.

Ivens, A.Mayans, O.Szadkowski, H.Jurgens, C.Wilmanns, M.Kirschner, K.

(2002) Eur J Biochem 269: 1145-1153

  • DOI: 10.1046/j.1432-1033.2002.02745.x
  • Primary Citation of Related Structures:  
    1JCM

  • PubMed Abstract: 
  • The aim of this study was to increase the stability of the thermolabile (betaalpha)8-barrel enzyme indoleglycerol phosphate synthase from Escherichia coli by the introduction of disulfide bridges. For the design of such variants, we selected two out of 12 candidates, in which newly introduced cysteines potentially form optimal disulfide bonds ...

    The aim of this study was to increase the stability of the thermolabile (betaalpha)8-barrel enzyme indoleglycerol phosphate synthase from Escherichia coli by the introduction of disulfide bridges. For the design of such variants, we selected two out of 12 candidates, in which newly introduced cysteines potentially form optimal disulfide bonds. These variants avoid short-range connections, substitutions near catalytic residues, and crosslinks between the new and the three parental cysteines. The variant linking residues 3 and 189 fastens the N-terminus to the (betaalpha)8-barrel. The rate of thermal inactivation at 50 degrees C of this variant with a closed disulfide bridge is 65-fold slower than that of the reference dithiol form, but only 13-fold slower than that of the parental protein. The near-ultraviolet CD spectrum, the reactivity of parental buried cysteines with Ellman's reagent as well as the decreased turnover number indicate that the protein structure is rigidified. To confirm these data, we have solved the X-ray structure to 2.1-A resolution. The second variant was designed to crosslink the terminal modules betaalpha1 and betaalpha8. However, not even the dithiol form acquired the native fold, possibly because one of the targeted residues is solvent-inaccessible in the parental protein.


    Organizational Affiliation

    Universität zu Köln, Institut für Biochemie, Köln, Germany. andreas.ivens@uni-koeln.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INDOLE-3-GLYCEROL-PHOSPHATE SYNTHASEA [auth P]259Escherichia coliMutation(s): 2 
EC: 4.1.1.48 (PDB Primary Data), 5.3.1.24 (UniProt)
UniProt
Find proteins for P00909 (Escherichia coli (strain K12))
Explore P00909 
Go to UniProtKB:  P00909
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00909
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
137
Query on 137

Download Ideal Coordinates CCD File 
H [auth P]1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE
C12 H18 N O9 P
AULMJMUNCOBRHC-MXWKQRLJSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth P],
C [auth P],
D [auth P],
E [auth P],
F [auth P],
B [auth P],
C [auth P],
D [auth P],
E [auth P],
F [auth P],
G [auth P]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.241 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.638α = 90
b = 81.638β = 90
c = 156.745γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2021-10-27
    Changes: Data collection, Database references, Derived calculations