Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.10 kDa 
• Atom Count: 3079 
• Modelled Residue Count: 357 
• Deposited Residue Count: 364 
• Unique protein chains: 1

1T1I

High Resolution Crystal Structure of Mutant W129A of Kumamolisin, a Sedolisin Type Proteinase (previously called Kumamolysin or KSCP)

• PDB DOI: 10.2210/pdb1T1I/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. MN-32
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-04-16 Released: 2004-08-03 
• Deposition Author(s): Comellas-Bigler, M., Maskos, K., Huber, R., Oyama, H., Oda, K., Bode, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.207 
• R-Value Work: 0.183 

Literature

1.2 a crystal structure of the serine carboxyl proteinase pro-kumamolisin: structure of an intact pro-subtilase

Comellas-Bigler, M., Maskos, K., Huber, R., Oyama, H., Oda, K., Bode, W.

(2004) Structure 12: 1313-1323

• PubMed: 15242607 
• DOI: 10.1016/j.str.2004.04.013
• Primary Citation of Related Structures:  
  1T1E, 1T1G, 1T1I


• PubMed Abstract: 
  

Kumamolisin, an extracellular proteinase derived from an acido/thermophilic Bacillus, belongs to the sedolisin family of endopeptidases characterized by a subtilisin-like fold and a Ser-Glu-Asp catalytic triad. In kumamolisin, the Asp82 carboxylate hydrogen bonds to Glu32-Trp129, which might act as a proton sink stabilizing the catalytic residues. The 1.2/1.3 A crystal structures of the Glu32-->Ala and Trp129-->Ala mutants show that both mutations affect the active-site conformation, causing a 95% activity decrease. In addition, the 1.2 A crystal structure of the Ser278-->Ala mutant of pro-kumamolisin was determined. The prodomain exhibits a half-beta sandwich core docking to the catalytic domain similarly as the equivalent subtilisin prodomains in their catalytic-domain complexes. This pro-kumamolisin structure displays, for the first time, the uncleaved linker segment running across the active site and connecting the prodomain with the properly folded catalytic domain. The structure strongly points to an initial intramolecular activation cleavage in subtilases, as presumed for pro-subtilisin and pro-furin.

---

Organizational Affiliation: 

Department of Structure Research, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18a, D-82152 Martinsried, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
kumamolisin	A	364	Bacillus sp. MN-32	Mutation(s): 1  Gene Names: kscp
UniProt
Find proteins for Q8RR56 (Bacillus sp. MN-32) Explore Q8RR56  Go to UniProtKB:  Q8RR56

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.207 
• R-Value Work: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.89	α = 90
b = 78.83	β = 106.41
c = 49.03	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-16 
• Released Date: 2004-08-03 
Deposition Author(s): Comellas-Bigler, M., Maskos, K., Huber, R., Oyama, H., Oda, K., Bode, W.

Revision History  

• Version 1.0: 2004-08-03
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations