4NSY

Wild-type lysobacter enzymogenes lysc endoproteinase covalently inhibited by TLCK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole.

Asztalos, P.Muller, A.Holke, W.Sobek, H.Rudolph, M.G.

(2014) Acta Crystallogr.,Sect.D 70: 1832-1843

  • DOI: 10.1107/S1399004714008463
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lysobacter enzymogenes lysyl endoproteinase (LysC) is a trypsin-type serine protease with a high pH optimum that hydrolyses all Lys-Xaa peptide bonds. The high specificity of LysC renders it useful for biotechnological purposes. The K30R variant of a ...

    Lysobacter enzymogenes lysyl endoproteinase (LysC) is a trypsin-type serine protease with a high pH optimum that hydrolyses all Lys-Xaa peptide bonds. The high specificity of LysC renders it useful for biotechnological purposes. The K30R variant of a related lysyl endoproteinase from Achromobacter lyticus has favourable enzymatic properties that might be transferrable to LysC. To visualize structural differences in the substrate-binding sites, the crystal structures of wild-type and the K30R variant of LysC were determined. The mutation is located at a distance of 12 Å from the catalytic triad and subtly changes the surface properties of the substrate-binding site. The high pH optimum of LysC can be attributed to electrostatic effects of an aromatic Tyr/His stack on the catalytic aspartate and is a general feature of this enzyme subfamily. LysC crystals in complex with the covalent inhibitor N(α)-p-tosyl-lysyl chloromethylketone yielded data to 1.1 and 0.9 Å resolution, resulting in unprecedented precision of the active and substrate-binding sites for this enzyme subfamily. Error estimates on bond lengths and difference electron density indicate that instead of the expected oxyanion a hydroxyl group binds to the partially solvent-exposed oxyanion hole. Protonation of the alkoxide catalytic intermediate might be a recurring feature during serine protease catalysis.


    Organizational Affiliation

    Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysyl endopeptidase
A, B
275Lysobacter enzymogenesMutation(s): 0 
EC: 3.4.21.50
Find proteins for Q7M135 (Lysobacter enzymogenes)
Go to UniProtKB:  Q7M135
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2OY
Query on 2OY

Download SDF File 
Download CCD File 
A, B
N-[(2S,3S)-7-amino-1-chloro-2-hydroxyheptan-3-yl]-4-methylbenzenesulfonamide (Bound Form)
Tosyllysine Chloromethyl Ketone (Bound Form)
C14 H23 Cl N2 O3 S
HBYAITRXPLQDLO-UONOGXRCSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001217 (2OY)
Query on PRD_001217
A,BN-[(2S,3S)-7-AMINO-1-CHLORO-2-HYDROXYHEPTAN-3-YL]-4-METHYLBENZENESULFONAMIDE (BOUND FORM)Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.579α = 90.00
b = 135.810β = 97.19
c = 45.587γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-07-09
    Type: Database references
  • Version 1.2: 2014-09-24
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description