5I8F

Crystal structure of St. John's wort Hyp-1 protein in complex with melatonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin.

Sliwiak, J.Dauter, Z.Jaskolski, M.

(2016) Front Plant Sci 7: 668-668

  • DOI: 10.3389/fpls.2016.00668
  • Also Cited By: 5MXW, 5MXB

  • PubMed Abstract: 
  • Hyp-1, a PR-10-fold protein from Hypericum perforatum, was crystallized in complex with melatonin (MEL). The structure confirms the conserved protein fold and the presence of three unusual ligand binding sites, two of which are internal chambers (1,2 ...

    Hyp-1, a PR-10-fold protein from Hypericum perforatum, was crystallized in complex with melatonin (MEL). The structure confirms the conserved protein fold and the presence of three unusual ligand binding sites, two of which are internal chambers (1,2), while the third one (3) is formed as an invagination of the protein surface. The MEL ligand in site 1 is well defined while that in site 3 seems to be rotating between the side chains of Lys33 and Tyr150 that act as a molecular vise. The patch of electron density in site 2 does not allow unambiguous modeling of a melatonin molecule but suggests a possible presence of its degradation product. This pattern of ligand occupation is reproducible in repeated crystallization/structure determination experiments. Although the binding of melatonin by Hyp-1 does not appear to be very strong (for example, MEL cannot displace the artificial fluorescence probe ANS), it is strong enough to suggest a physiological role of this interaction. For example, trans-zeatin, which is a common ligand of PR-10 proteins, does not overcompete melatonin for binding to Hyp-1 as it does not affect the crystallization process of the Hyp-1/MEL complex, and among a number of potential natural mediators tested, melatonin was the only one to form a crystalline complex with Hyp-1 with the use of standard crystallization screens. Hyp-1 is the second protein in the Protein Data Bank for which melatonin binding has been demonstrated crystallographically, the first one being human quinone reductase.


    Related Citations: 
    • Crystal Structure Of Vigna Radiata Cytokinin-Specific Binding Protein In Complex With Zeatin.
      Pasternak, O.,Bujacz, G.D.,Fujimoto, Y.,Hashimoto, Y.,Jelen, F.,Otlewski, J.,Sikorski, M.M.,Jaskolski, M.
      (2006) Plant Cell 18: 2622
    • Likelihood-Based Molecular-Replacement Solution For A Highly Pathological Crystal With Tetartohedral Twinning And Sevenfold Translational Noncrystallographic Symmetry.
      Sliwiak, J.,Jaskolski, M.,Dauter, Z.,Mccoy, A.J.,Read, R.J.
      (2014) Acta Crystallogr.,Sect.D 70: 471
    • Lupinus Luteus Pathogenesis-Related Protein As A Reservoir For Cytokinin.
      Fernandes, H.,Pasternak, O.,Bujacz, G.,Bujacz, A.,Sikorski, M.M.,Jaskolski, M.
      (2008) J.Mol.Biol. 378: 1040
    • The Landscape Of Cytokinin Binding By A Plant Nodulin.
      Ruszkowski, M.,Szpotkowski, K.,Sikorski, M.,Jaskolski, M.
      (2013) Acta Crystallogr.,Sect.D 69: 2365
    • Crystal Structures Of Two Homologous Pathogenesis-Related Proteins From Yellow Lupine.
      Biesiadka, J.,Bujacz, G.,Sikorski, M.M.,Jaskolski, M.
      (2002) J.Mol.Biol. 319: 1223
    • Crystal Structure Of Hyp-1, A St. John'S Wort Protein Implicated In The Biosynthesis Of Hypericin.
      Michalska, K.,Fernandes, H.,Sikorski, M.,Jaskolski, M.
      (2010) J.Struct.Biol. 169: 161
    • Ans Complex Of St John'S Wort Pr-10 Protein With 28 Copies In The Asymmetric Unit: A Fiendish Combination Of Pseudosymmetry With Tetartohedral Twinning.
      Sliwiak, J.,Dauter, Z.,Kowiel, M.,Mccoy, A.J.,Read, R.J.,Jaskolski, M.
      (2015) Acta Crystallogr.,Sect.D 71: 829
    • Cytokinin-Induced Structural Adaptability Of A Lupinus Luteus Pr-10 Protein.
      Fernandes, H.,Bujacz, A.,Bujacz, G.,Jelen, F.,Jasinski, M.,Kachlicki, P.,Otlewski, J.,Sikorski, M.M.,Jaskolski, M.
      (2009) Febs J. 276: 1596
    • Specific Binding Of Gibberellic Acid By Cytokinin-Specific Binding Proteins: A New Aspect Of Plant Hormone-Binding Proteins With The Pr-10 Fold.
      Ruszkowski, M.,Sliwiak, J.,Ciesielska, A.,Barciszewski, J.,Sikorski, M.,Jaskolski, M.
      (2014) Acta Crystallogr.,Sect.D 70: 2032
    • Crystallographic And Cd Probing Of Ligand-Induced Conformational Changes In A Plant Pr-10 Protein.
      Sliwiak, J.,Dolot, R.,Michalska, K.,Szpotkowski, K.,Bujacz, G.,Sikorski, M.,Jaskolski, M.
      (2016) J.Struct.Biol. 193: 55


    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan, Poland.,Synchrotron Radiation Research Section, National Cancer Institute, Argonne National Laboratory, Argonne IL, USA.,Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland; Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University in PoznańPoznań, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenolic oxidative coupling protein
A
165Hypericum kouytchenseMutation(s): 0 
Gene Names: hyp1
Find proteins for E9JSA3 (Hypericum kouytchense)
Go to UniProtKB:  E9JSA3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ML1
Query on ML1

Download SDF File 
Download CCD File 
A
N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide
Melatonin
C13 H16 N2 O2
DRLFMBDRBRZALE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.128 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 60.860α = 90.00
b = 89.639β = 90.00
c = 76.410γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
U.S. Department of Energy, Office of Science, Office of Basic Energy SciencesUnited StatesW-31-109-Eng-38
National Science CentrePoland2013/10/M/NZ1/00251

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Database references
  • Version 1.2: 2018-08-08
    Type: Data collection, Database references
  • Version 1.3: 2019-01-23
    Type: Data collection, Database references, Source and taxonomy