High resolution crystal structure of a thermostable serine-carboxyl type proteinase, kumamolisin (kscp)

Experimental Data Snapshot

  • Resolution: 1.38 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

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This is version 1.3 of the entry. See complete history


The 1.4 A Crystal Structure of Kumamolysin. A Thermostable Serine-Carboxyl-Type Proteinase

Comellas-Bigler, M.Fuentes-Prior, P.Maskos, K.Huber, R.Oyama, H.Uchida, K.Dunn, B.M.Oda, K.Bode, W.

(2002) Structure 10: 865

  • DOI: https://doi.org/10.1016/s0969-2126(02)00772-4
  • Primary Citation of Related Structures:  
    1GT9, 1GTG, 1GTJ, 1GTL

  • PubMed Abstract: 

    Kumamolysin is a thermostable endopeptidase from Bacillus novosp. MN-32, exhibiting maximal proteolytic activity around pH 3. It belongs to the newly identified family of serine-carboxyl proteinases, which also includes CLN2, a human lysosomal homolog recently implicated in a fatal neurodegenerative disease. Kumamolysin and its complexes with two aldehyde inhibitors were crystallized, and their three-dimensional structures were solved and refined with X-ray data to 1.4 A resolution. As its Pseudomonas homolog, kumamolysin exhibits a Ser/Glu/Asp catalytic triad with particularly short interconnecting hydrogen bonds and an oxyanion hole enabling the reactive serine to attack substrate peptide bonds at quite acidic pH. An additional Glu/Trp pair, unique to kumamolysin, might further facilitate proton delocalization during nucleophilic attack, in particular at high temperature.

  • Organizational Affiliation

    Abteilung für Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18 a, D82152, Planegg-Martinsried, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B [auth 2]
357Bacillus subtilisMutation(s): 0 
Find proteins for Q8RR56 (Bacillus sp. MN-32)
Explore Q8RR56 
Go to UniProtKB:  Q8RR56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RR56
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.38 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.86α = 90
b = 78.25β = 90
c = 73.53γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description