1GTL

The thermostable serine-carboxyl type proteinase, kumamolisin (KSCP) - complex with Ac-Ile-Pro-Phe-cho


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • Primary Citation of Related Structures:  1GT9, 1GTG, 1GTJ

  • 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 homolo ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KUMAMOLYSIN
1, 2
357Bacillus sp. MN-32Gene Names: kscp
Find proteins for Q8RR56 (Bacillus sp. MN-32)
Go to UniProtKB:  Q8RR56
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALDEHYDE INHIBITOR
3, 4
4N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
1, 2
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
1, 2
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000240
Query on PRD_000240
3,4N-acetyl-L-isoleucyl-L-prolyl-L-PhenylalaninalPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.030α = 90.00
b = 78.300β = 98.45
c = 73.170γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
AMoREphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Type: Other
  • Version 1.3: 2016-12-21
    Type: Source and taxonomy, Structure summary