6TXG | pdb_00006txg

Proteinase K in complex with a "half sandwich"-type Ru(II) coordination compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 
    0.168 (Depositor), 0.169 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1007/s00775-020-01786-z
  • Primary Citation Related Structures: 
    6TVL, 6TXG

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 30.16 kDa 
  • Atom Count: 2,378 
  • Modeled Residue Count: 279 
  • Deposited Residue Count: 279 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 0 
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NYN
(Subject of Investigation/LOI)

Query on NYN



Download:Ideal Coordinates CCD File
H [auth A],
J [auth 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
TFS

Query on TFS



Download:Ideal Coordinates CCD File
K [auth A]trifluoromethanesulfonic acid
C H F3 O3 S
ITMCEJHCFYSIIV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3

Query on NO3



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free:  0.168 (Depositor), 0.169 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.708α = 90
b = 67.708β = 90
c = 107.314γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary