6TVL

Hen Egg White Lysozyme in complex with a "half sandwich"-type Ru(II) coordination compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-resolution crystal structures of a "half sandwich"-type Ru(II) coordination compound bound to hen egg-white lysozyme and proteinase K.

Chiniadis, L.Bratsos, I.Bethanis, K.Karpusas, M.Giastas, P.Papakyriakou, A.

(2020) J Biol Inorg Chem 25: 635-645

  • DOI: 10.1007/s00775-020-01786-z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The high-resolution X-ray crystal structures of the adducts formed between the "half sandwich"-type Ru(II) coordination compound [Ru II (1,4,7-trithiacyclononane)(ethane-1,2-diamine)Cl] + and two proteins, namely hen egg-white ...

    The high-resolution X-ray crystal structures of the adducts formed between the "half sandwich"-type Ru(II) coordination compound [Ru II (1,4,7-trithiacyclononane)(ethane-1,2-diamine)Cl] + and two proteins, namely hen egg-white lysozyme and proteinase K, are presented. The structures unveil that upon reaction with both enzymes the Ru(II) compound is coordinated by solvent-exposed aspartate residues after releasing the chloride ligand (Asp101 in lysozyme, Asp200 and Asp260 in proteinase K), while retaining the two chelating ligands. The adduct with Asp101 residue at the catalytic cleft of lysozyme is accompanied by residue-specific conformational changes to accommodate the Ru(II) fragment, whereas the complexes bound at the two calcium-binding sites of proteinase K revealed minimal structural perturbation of the enzyme. To the best of our knowledge, proteinase K is used here for the first time as a model system of protein metalation and these are the first X-ray crystal structures of protein adducts of a Ru(II) coordination compound that maintains its coordination sphere almost intact upon binding. Our data demonstrate the role of ligands in stabilizing the protein adducts via hydrophobic/aromatic or hydrogen-bonding interactions, as well as their underlying role in the selection of specific sites on the electrostatic potential surface of the enzymes.


    Organizational Affiliation

    Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", 15341, Athens, Greece. thpap@bio.demokritos.gr.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme CA129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NYN
Query on NYN

Download CCD File 
A
chlorido(1,2-diaminoethane-k2N,N')(1,4,7-trithiacyclononane-k3S,S',S'')ruthenium(II) trifluoromethanesulfonate
C8 H16 N2 Ru S3
ZNOIBYRQMPADCX-UHFFFAOYSA-N
 Ligand Interaction
TFS
Query on TFS

Download CCD File 
A
trifluoromethanesulfonic acid
C H F3 O3 S
ITMCEJHCFYSIIV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.27α = 90
b = 79.27β = 90
c = 35.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references