2ZRQ | pdb_00002zrq

Crystal structure of S324A-subtilisin

• PDB DOI: https://doi.org/10.2210/pdb2ZRQ/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-08-28 Released: 2009-03-03 
• Deposition Author(s): Tanaka, S., Takeuchi, Y., Matsumura, H., Koga, Y., Takano, K., Kanaya, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Tk-subtilisin folded without propeptide: requirement of propeptide for acceleration of folding

Tanaka, S., Takeuchi, Y., Matsumura, H., Koga, Y., Takano, K., Kanaya, S.

(2008) FEBS Lett 582: 3875-3878

• PubMed: 18951896 
• DOI: https://doi.org/10.1016/j.febslet.2008.10.025
• Primary Citation Related Structures: 
  2ZRQ


• PubMed Abstract: 
  

  Tk-subtilisin (a subtilisin homologue from Thermococcus kodakaraensis) is matured from Pro-Tk-subtilisin upon autoprocessing and degradation of Tk-propeptide. To analyze the folding mechanism of Tk-subtilisin, the crystal structure of the active site mutant of Tk-subtilisin (S324A-subtilisin*), which was refolded in the presence of Ca2+ and absence of Tk-propeptide, was determined at 2.16A resolution. This structure is essentially the same as that of Tk-subtilisin matured from Pro-Tk-subtilisin. S324A-subtilisin* was refolded with a rate constant of 0.17 and 1.8min(-1) at 30 degrees C in the absence and presence of Tk-propeptide, respectively, indicating that Tk-subtilisin does not require Tk-propeptide for folding but requires it for acceleration of folding.

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Organizational Affiliation: 
• Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.18 kDa 
• Atom Count: 2,509 
• Modeled Residue Count: 318 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tk-subtilisin	A	329	Thermococcus kodakarensis KOD1	Mutation(s): 1  Gene Names: TK1675 EC: 3.4.21.62 (PDB Primary Data), 3.4.21 (UniProt)
UniProt
Find proteins for P58502 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore P58502  Go to UniProtKB:  P58502

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.188	α = 90
b = 60.925	β = 90
c = 92.277	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Tanaka, S., Takeuchi, Y., Matsumura, H., Koga, Y., Takano, K., Kanaya, S.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary