Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.52 kDa 
• Atom Count: 1,026 
• Modelled Residue Count: 123 
• Deposited Residue Count: 131 
• Unique protein chains: 1

 4K1V

Crystal structure of delta5-3-ketosteroid isomerase containing Y16F and Y57F mutations

• PDB DOI:  https://doi.org/10.2210/pdb4K1V/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-04-05 Released: 2013-07-31 
• Deposition Author(s): Cha, H.J., Jang, D.S., Kim, Y.G., Hong, B.H., Woo, J.S., Choi, K.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.200 

Literature

Rescue of deleterious mutations by the compensatory Y30F mutation in ketosteroid isomerase

Cha, H.J., Jang, D.S., Kim, Y.G., Hong, B.H., Woo, J.S., Kim, K.T., Choi, K.Y.

(2013) Mol Cells 36: 39-46

• PubMed: 23740430 
• DOI: https://doi.org/10.1007/s10059-013-0013-1
• Primary Citation of Related Structures:  
  4K1U, 4K1V


• PubMed Abstract: 
  

Proteins have evolved to compensate for detrimental mutations. However, compensatory mechanisms for protein defects are not well understood. Using ketosteroid isomerase (KSI), we investigated how second-site mutations could recover defective mutant function and stability. Previous results revealed that the Y30F mutation rescued the Y14F, Y55F and Y14F/Y55F mutants by increasing the catalytic activity by 23-, 3- and 1.3-fold, respectively, and the Y55F mutant by increasing the stability by 3.3 kcal/mol. To better understand these observations, we systematically investigated detailed structural and thermodynamic effects of the Y30F mutation on these mutants. Crystal structures of the Y14F/Y30F and Y14F/Y55F mutants were solved at 2.0 and 1.8 previoulsy solved structures of wild-type and other mutant KSIs. Structural analyses revealed that the Y30F mutation partially restored the active-site cleft of these mutant KSIs. The Y30F mutation also increased Y14F and Y14F/Y55F mutant stability by 3.2 and 4.3 kcal/mol, respectively, and the melting temperatures of the Y14F, Y55F and Y14F/Y55F mutants by 6.4°C, 5.1°C and 10.0°C, respectively. Compensatory effects of the Y30F mutation on stability might be due to improved hydrophobic interactions because removal of a hydroxyl group from Tyr30 induced local compaction by neighboring residue movement and enhanced interactions with surrounding hydrophobic residues in the active site. Taken together, our results suggest that perturbed active-site geometry recovery and favorable hydrophobic interactions mediate the role of Y30F as a secondsite suppressor.

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Organizational Affiliation: 

Department of Life Science, WCU Program, Pohang University of Science and Technology, Pohang, 790-784, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid Delta-isomerase	A	131	Pseudomonas putida	Mutation(s): 2  Gene Names: ksi EC: 5.3.3.1
UniProt
Find proteins for P07445 (Pseudomonas putida) Explore P07445  Go to UniProtKB:  P07445

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.200 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.347	α = 90
b = 94.723	β = 90
c = 73.886	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Cha, H.J., Jang, D.S., Kim, Y.G., Hong, B.H., Woo, J.S., Choi, K.Y.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references