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

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.128 

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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
  • Primary Citation of Related Structures:  

  • 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), while the third one (3) is formed as an invagination of the protein surface ...

    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 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 D Biol Crystallogr 71: 829
    • 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 D Biol Crystallogr 70: 471
    • 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
    • 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
    • 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
    • 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
    • The Landscape Of Cytokinin Binding By A Plant Nodulin.
      Ruszkowski, M., Szpotkowski, K., Sikorski, M., Jaskolski, M.
      (2013) Acta Crystallogr D Biol Crystallogr 69: 2365
    • 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 D Biol Crystallogr 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 SciencesPoznan, Poland; Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University in PoznańPoznań, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenolic oxidative coupling proteinA165Hypericum perforatumMutation(s): 0 
Gene Names: hyp1
Find proteins for E9JSA3 (Hypericum kouytchense)
Explore E9JSA3 
Go to UniProtKB:  E9JSA3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9JSA3
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on ML1

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]
C13 H16 N2 O2
 Ligand Interaction
Query on GOL

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A]
C3 H8 O3
 Ligand Interaction
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A]
 Ligand Interaction
Query on UNL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
Unknown ligand
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.86α = 90
b = 89.639β = 90
c = 76.41γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesW-31-109-Eng-38
National Science CentrePoland2013/10/M/NZ1/00251

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.3: 2019-01-23
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.4: 2022-03-30
    Changes: Author supporting evidence, Database references, Derived calculations