1GTJ

Crystal structure of the thermostable serine-carboxyl type proteinase, kumamolisin (KSCP) - complex with Ac-Ile-Ala-Phe-cho


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KUMAMOLYSINA [auth 1],
B [auth 2]
357Bacillus sp. MN-32Mutation(s): 0 
UniProt
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
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALDEHYDE INHIBITORC [auth 3],
D [auth 4]
4synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.76α = 90
b = 78.17β = 98.11
c = 72.99γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

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: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Changes: Other
  • Version 1.3: 2017-02-08
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2018-02-28
    Changes: Advisory, Data collection
  • Version 1.5: 2019-09-04
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description