3ie5

From Proteopedia

(Difference between revisions)

Revision as of 15:57, 1 November 2023

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

Structural highlights

3ie5 is a 2 chain structure with sequence from Hypericum perforatum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.688Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8H1L1_HYPPE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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 J Struct Biol. 2010 Feb;169(2):161-71. Epub 2009 Oct 21. PMID:19853038^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Michalska K, Fernandes H, Sikorski M, Jaskolski M. Crystal structure of Hyp-1, a St. John's wort protein implicated in the biosynthesis of hypericin. J Struct Biol. 2010 Feb;169(2):161-71. Epub 2009 Oct 21. PMID:19853038 doi:10.1016/j.jsb.2009.10.008

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ie5"

@@ Line 3: / Line 3: @@
 <StructureSection load='3ie5' size='340' side='right'caption='[[3ie5]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ie5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hyppe Hyppe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IE5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ie5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hypericum_perforatum Hypericum perforatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IE5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.688&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bv1|1bv1]], [[1icx|1icx]], [[1ifv|1ifv]], [[1xdf|1xdf]], [[2flh|2flh]], [[2qim|2qim]], [[3e85|3e85]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hyp-1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=65561 HYPPE])</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ie5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ie5 OCA], [https://pdbe.org/3ie5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ie5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ie5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ie5 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8H1L1_HYPPE Q8H1L1_HYPPE]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Hyppe]]
+[[Category: Hypericum perforatum]]
 [[Category: Large Structures]]
-[[Category: Fernandes, H]]
+[[Category: Fernandes H]]
-[[Category: Jaskolski, M]]
+[[Category: Jaskolski M]]
-[[Category: Michalska, K]]
+[[Category: Michalska K]]
-[[Category: Sikorski, M M]]
+[[Category: Sikorski MM]]
-[[Category: Allergy]]
-[[Category: Biosynthetic protein]]
-[[Category: Cytokinin]]
-[[Category: Depression]]
-[[Category: Hypericin]]
-[[Category: Pathogenesis-related protein]]
-[[Category: Peg]]
-[[Category: Plant defense]]
-[[Category: Plant hormone]]
-[[Category: Plant protein]]
-[[Category: Polyethylene glycol]]
-[[Category: Pr-10 protein]]
-[[Category: St john's wort]]

3ie5

From Proteopedia

Revision as of 15:57, 1 November 2023

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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