2vne

From Proteopedia

(Difference between revisions)

Current revision

The X-ray structure of Norcoclaurine synthase from Thalictrum flavum

Structural highlights

2vne is a 2 chain structure with sequence from Thalictrum flavum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.72Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NCS_THLFG Involved in the biosynthesis of the common precursor of all benzylisoquinoline alkaloids such as morphine, sanguinarine, codeine or berberine. Condenses dopamine and 4-hydroxyphenylacetaldehyde.^[1] ^[2] ^[3]

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

The enzyme norcoclaurine synthase (NCS) catalyzes the stereospecific Pictet-Spengler cyclization between dopamine and 4-hydroxyphenylacetaldehyde, the key step in the benzylisoquinoline alkaloid biosynthetic pathway. The crystallographic structure of norcoclaurine synthase from Thalictrum flavum in its complex with dopamine substrate and the nonreactive substrate analogue 4-hydroxybenzaldehyde has been solved at 2.1A resolution. NCS shares no common features with the functionally correlated "Pictet-Spenglerases" that catalyze the first step of the indole alkaloids pathways and conforms to the overall fold of the Bet v1-like protein. The active site of NCS is located within a 20-A-long catalytic tunnel and is shaped by the side chains of a tyrosine, a lysine, an aspartic, and a glutamic acid. The geometry of the amino acid side chains with respect to the substrates reveals the structural determinants that govern the mechanism of the stereoselective Pictet-Spengler cyclization, thus establishing an excellent foundation for the understanding of the finer details of the catalytic process. Site-directed mutations of the relevant residues confirm the assignment based on crystallographic findings.

Structural basis of enzymatic (S)-norcoclaurine biosynthesis.,Ilari A, Franceschini S, Bonamore A, Arenghi F, Botta B, Macone A, Pasquo A, Bellucci L, Boffi A J Biol Chem. 2009 Jan 9;284(2):897-904. Epub 2008 Nov 12. PMID:19004827^[4]

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

References

↑ Luk LY, Bunn S, Liscombe DK, Facchini PJ, Tanner ME. Mechanistic studies on norcoclaurine synthase of benzylisoquinoline alkaloid biosynthesis: an enzymatic Pictet-Spengler reaction. Biochemistry. 2007 Sep 4;46(35):10153-61. Epub 2007 Aug 15. PMID:17696451 doi:http://dx.doi.org/10.1021/bi700752n
↑ Berkner H, Engelhorn J, Liscombe DK, Schweimer K, Wohrl BM, Facchini PJ, Rosch P, Matecko I. High-yield expression and purification of isotopically labeled norcoclaurine synthase, a Bet v 1-homologous enzyme, from Thalictrum flavum for NMR studies. Protein Expr Purif. 2007 Dec;56(2):197-204. Epub 2007 Aug 24. PMID:17900926 doi:http://dx.doi.org/10.1016/j.pep.2007.07.010
↑ Berkner H, Schweimer K, Matecko I, Rosch P. Conformation, catalytic site, and enzymatic mechanism of the PR10 allergen-related enzyme norcoclaurine synthase. Biochem J. 2008 Jul 15;413(2):281-90. doi: 10.1042/BJ20080306. PMID:18384289 doi:http://dx.doi.org/10.1042/BJ20080306
↑ Ilari A, Franceschini S, Bonamore A, Arenghi F, Botta B, Macone A, Pasquo A, Bellucci L, Boffi A. Structural basis of enzymatic (S)-norcoclaurine biosynthesis. J Biol Chem. 2009 Jan 9;284(2):897-904. Epub 2008 Nov 12. PMID:19004827 doi:10.1074/jbc.M803738200

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/2vne"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2vne.png|left|200px]]
-<!--
+==The X-ray structure of Norcoclaurine synthase from Thalictrum flavum==
-The line below this paragraph, containing "STRUCTURE_2vne", creates the "Structure Box" on the page.
+<StructureSection load='2vne' size='340' side='right'caption='[[2vne]], [[Resolution|resolution]] 2.72&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2vne]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thalictrum_flavum Thalictrum flavum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VNE FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.72&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2vne|  PDB=2vne  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vne OCA], [https://pdbe.org/2vne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vne RCSB], [https://www.ebi.ac.uk/pdbsum/2vne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vne ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NCS_THLFG NCS_THLFG] Involved in the biosynthesis of the common precursor of all benzylisoquinoline alkaloids such as morphine, sanguinarine, codeine or berberine. Condenses dopamine and 4-hydroxyphenylacetaldehyde.<ref>PMID:17696451</ref> <ref>PMID:17900926</ref> <ref>PMID:18384289</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vn/2vne_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <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/main_output.php?pdb_ID=2vne ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The enzyme norcoclaurine synthase (NCS) catalyzes the stereospecific Pictet-Spengler cyclization between dopamine and 4-hydroxyphenylacetaldehyde, the key step in the benzylisoquinoline alkaloid biosynthetic pathway. The crystallographic structure of norcoclaurine synthase from Thalictrum flavum in its complex with dopamine substrate and the nonreactive substrate analogue 4-hydroxybenzaldehyde has been solved at 2.1A resolution. NCS shares no common features with the functionally correlated "Pictet-Spenglerases" that catalyze the first step of the indole alkaloids pathways and conforms to the overall fold of the Bet v1-like protein. The active site of NCS is located within a 20-A-long catalytic tunnel and is shaped by the side chains of a tyrosine, a lysine, an aspartic, and a glutamic acid. The geometry of the amino acid side chains with respect to the substrates reveals the structural determinants that govern the mechanism of the stereoselective Pictet-Spengler cyclization, thus establishing an excellent foundation for the understanding of the finer details of the catalytic process. Site-directed mutations of the relevant residues confirm the assignment based on crystallographic findings.
-===THE X-RAY STRUCTURE OF NORCOCLAURINE SYNTHASE FROM THALICTRUM FLAVUM===
+Structural basis of enzymatic (S)-norcoclaurine biosynthesis.,Ilari A, Franceschini S, Bonamore A, Arenghi F, Botta B, Macone A, Pasquo A, Bellucci L, Boffi A J Biol Chem. 2009 Jan 9;284(2):897-904. Epub 2008 Nov 12. PMID:19004827<ref>PMID:19004827</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19004827}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vne" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19004827 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19004827}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VNE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thalictrum_flavum Thalictrum flavum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VNE OCA].
-==Reference==
-Structural basis of enzymatic S-norcoclaurine biosynthesis., Ilari A, Franceschini S, Bonamore A, Arenghi F, Botta B, Macone A, Pasquo A, Bellucci L, Boffi A, J Biol Chem. 2008 Nov 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19004827 19004827]
-Cloning, expression, crystallization and preliminary X-ray data analysis of norcoclaurine synthase from Thalictrum flavum., Pasquo A, Bonamore A, Franceschini S, Macone A, Boffi A, Ilari A, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Apr 1;64(Pt, 4):281-3. Epub 2008 Mar 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18391427 18391427]
-[[Category: Single protein]]
 [[Category: Thalictrum flavum]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Boffi A]]
-[[Category: Biosynthesis of benzylisoquinoline alkaloid]]
+[[Category: Bonamore A]]
-[[Category: Lyase]]
+[[Category: Franceschini S]]
-[[Category: Norcoclaurine synthase]]
+[[Category: Ilari A]]
+[[Category: Pasquo A]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 20:26:35 2009''

2vne

From Proteopedia

Current revision

The X-ray structure of Norcoclaurine synthase from Thalictrum flavum

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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