1N6D

Tricorn protease in complex with tetrapeptide chloromethyl ketone derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.285 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Navigation Inside a Protease: Substrate Selection and Product Exit in the Tricorn Protease from Thermoplasma acidophilum

Kim, J.-S.Groll, M.Musiol, H.-J.Behrendt, R.Kaiser, M.Moroder, L.Huber, R.Brandstetter, H.

(2002) J.Mol.Biol. 324: 1041-1050

  • Primary Citation of Related Structures:  1N6E, 1N6F

  • PubMed Abstract: 
  • The proposed pathway and mechanism of substrate entry and product egress in the hexameric D3 symmetric tricorn protease from Thermoplasma acidophilum were explored by crystallographic studies of ligand complexes and by structure-based mutagenesis. Ob ...

    The proposed pathway and mechanism of substrate entry and product egress in the hexameric D3 symmetric tricorn protease from Thermoplasma acidophilum were explored by crystallographic studies of ligand complexes and by structure-based mutagenesis. Obstruction of the pore within the 7-bladed beta-propeller (beta7) domain by alkylation or oxidation of an engineered double cysteine mutant strongly decreased enzymatic activities. In line herewith, the crystal structure of the tricorn protease in complex with a trideca-peptide inhibitor modifying the catalytic Ser965 revealed part of the peptide trapped inside the channel of the beta7 domain. The cysteine mutation widening the lumen of the 6-bladed beta-propeller (beta6) domain enhanced catalytic activity, which was restored to normal values after its alkylation. A charge reversal mutant at the putative anchor site of the substrate C terminus, R131E-R132E, drastically reduced the proteolytic activity. The complex crystal structure of a peptide inhibitor with a diketo group at the cleavage site mapped the substrate recognition site and confirmed the role of Arg131-Arg132 as an anchor site. Our results strongly suggest the wider beta7 domain to serve as a selective filter and guide of the substrate to the sequestered active site, while the narrower beta6 domain routes the product to the surface. Moreover, we identified the role of Arg131-Arg132 in anchoring the substrate C terminus.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D-82152 Planegg-Martinsried, Germany. jkim@biochem.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tricorn protease
A, B, C, D, E, F
1071Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)Gene Names: tri
EC: 3.4.21.-
Find proteins for P96086 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Go to UniProtKB:  P96086
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RVRK
G, H, I, J, K, L
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
CHM
Query on CHM

Download SDF File 
Download CCD File 
G, H, I, J, K, L
1,3-DICHLORO-PROPAN-2-ONE
CHLOROMETYL-KETONE
C3 H4 Cl2 O
SUNMBRGCANLOEG-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

Download SDF File 
Download CCD File 
G, H, I, J, K, L
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.285 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.440α = 90.00
b = 245.430β = 104.79
c = 159.400γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance