3ie5

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(Difference between revisions)

Revision as of 22:36, 5 August 2016

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 Hyppe. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , ,
Related:	1bv1, 1icx, 1ifv, 1xdf, 2flh, 2qim, 3e85
Gene:	hyp-1 (HYPPE)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of Hyp-1 protein from Hypericum perforatum (St John's wort) involved in hypericin biosynthesis==
 <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 [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IE5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ie5]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IE5 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1bv1|1bv1]], [[1icx|1icx]], [[1ifv|1ifv]], [[1xdf|1xdf]], [[2flh|2flh]], [[2qim|2qim]], [[3e85|3e85]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hyp-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=65561 Hypericum perforatum])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hyp-1 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ie5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ie5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ie5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ie5 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ie5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ie5 OCA], [http://pdbe.org/3ie5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ie5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ie5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ie5 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 16: / Line 17: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ie5 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3ie5" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hypericum perforatum]]
+[[Category: Hyppe]]
 [[Category: Fernandes, H]]
 [[Category: Jaskolski, M]]

3ie5

From Proteopedia

Revision as of 22:36, 5 August 2016

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

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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