3IE5

Crystal structure of Hyp-1 protein from Hypericum perforatum (St John's wort) involved in hypericin biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.688 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Hyp-1, a St. John's wort protein implicated in the biosynthesis of hypericin

Michalska, K.Fernandes, H.Sikorski, M.M.Jaskolski, M.

(2010) J.Struct.Biol. 169: 161-171

  • DOI: 10.1016/j.jsb.2009.10.008
  • Also Cited By: 5I8F, 4GY9, 3RWS

  • PubMed Abstract: 
  • Hypericin, a red-colored naphtodianthrone, is a natural product synthesized in the medicinal plant Hypericum perforatum, widely known as St. John's wort. Hypericin has been attracting a growing attention of the pharmaceutical industry because of its ...

    Hypericin, a red-colored naphtodianthrone, is a natural product synthesized in the medicinal plant Hypericum perforatum, widely known as St. John's wort. Hypericin has been attracting a growing attention of the pharmaceutical industry because of its potential application in various therapies, including the treatment of depression. In vivo, hypericin is synthesized by dimerization of emodin in a complicated multistep reaction that is reportedly catalyzed by a small (17.8kDa) protein, Hyp-1. Based on relatively low sequence similarity ( approximately 50%), Hyp-1 has been tentatively classified as a plant PR-10 (pathogenesis-related class 10) protein. Members of the PR-10 family are ubiquitous plant proteins associated with stress control and tissue differentiation but with no clearly understood molecular mechanism. They have, however, a well-defined folding canon, consisting of an extended antiparallel beta-sheet wrapped around a C-terminal alpha-helix, enclosing in the protein interior a huge cavity, in which various hydrophobic ligands can be bound. Apart from Hyp-1, only two other PR-10 members have been found to possess enzymatic activity (S-norcoclaurine synthase and TcmN aromatase/cyclase). In this paper, we report a high-resolution crystal structure of Hyp-1, confirming that it indeed has a PR-10 fold. The protein binds multiple polyethylene glycol molecules, some of which occupy the hydrophobic cavity. The crystallographic model illustrates a high degree of conformational adaptability of both interacting partners for efficient binding. We have been unable, however, to dimerize emodin to hypericin using Hyp-1 as biocatalyst. This puzzling result does not have a clear explanation at this time.


    Related Citations: 
    • Crystallization and preliminary crystallographic studies of Hyp-1, a St John's wort protein implicated in the biosynthesis of hypericin
      Fernandes, H.,Konieczna, M.,Kolodziejczyk, R.,Bujacz, G.,Sikorski, M.M.,Jaskolski, M.
      (2008) Acta Crystallogr.,Sect.F 64: 405
    • 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
    • X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy
      Gajhede, M.,Osmark, P.,Poulsen, F.M.,Ipsen, H.,Larsen, J.N.,Joost van Neerven, R.J.,Schou, C.,Lowenstein, H.,Spangfort, M.D.
      (1996) Nat.Struct.Mol.Biol. 3: 1040
    • 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 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
    • 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
    • Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass
      Pasternak, O.,Biesiadka, J.,Dolot, R.,Handschuh, L.,Bujacz, G.,Sikorski, M.M.,Jaskolski, M.
      (2005) Acta Crystallogr.,Sect.D 61: 99


    Organizational Affiliation

    Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenolic oxidative coupling protein Hyp-1
A, B
165Hypericum perforatumMutation(s): 0 
Gene Names: HYP1.1
Find proteins for Q8H1L1 (Hypericum perforatum)
Go to UniProtKB:  Q8H1L1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PE8
Query on PE8

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A
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.688 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.538α = 90.00
b = 76.713β = 90.00
c = 119.799γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
MAR345data collection
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Advisory, Refinement description