2vq5: Difference between revisions

Latest revision as of 01:27, 21 November 2024

X-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine and hydroxybenzaldehyde

Structural highlights

2vq5 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 2.09Å
Ligands:	ACT, CL, HBA, LDP, MSE
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:https://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:https://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:https://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

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1021/bi700752n

[2] 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:https://dx.doi.org/10.1016/j.pep.2007.07.010

[3] 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:https://dx.doi.org/10.1042/BJ20080306

[4] 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]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-==X-RAY STRUCTURE OF NORCOCLAURINE SYNTHASE FROM THALICTRUM FLAVUM IN COMPLEX WITH DOPAMINE AND HYDROXYBENZALDEHYDE==
+==X-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine and hydroxybenzaldehyde==
-<StructureSection load='2vq5' size='340' side='right' caption='[[2vq5]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
+<StructureSection load='2vq5' size='340' side='right'caption='[[2vq5]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vq5]] is a 2 chain structure with 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=2VQ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VQ5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vq5]] 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=2VQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VQ5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene>, <scene name='pdbligand=LDP:L-DOPAMINE'>LDP</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]] 2.09&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene>, <scene name='pdbligand=LDP:L-DOPAMINE'>LDP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vne|2vne]]</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=2vq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vq5 OCA], [https://pdbe.org/2vq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vq5 RCSB], [https://www.ebi.ac.uk/pdbsum/2vq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vq5 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-norcoclaurine_synthase (S)-norcoclaurine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.78 4.2.1.78] </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=2vq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vq5 OCA], [http://pdbe.org/2vq5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vq5 RCSB], [http://www.ebi.ac.uk/pdbsum/2vq5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vq5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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/vq/2vq5_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vq/2vq5_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 35: / Line 33: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Thalictrum flavum]]
-[[Category: Boffi, A]]
+[[Category: Boffi A]]
-[[Category: Bonamore, A]]
+[[Category: Bonamore A]]
-[[Category: Franceschini, S]]
+[[Category: Franceschini S]]
-[[Category: Ilari, A]]
+[[Category: Ilari A]]
-[[Category: Dopamine]]
-[[Category: Hydroxybenzaldehyde]]
-[[Category: Lyase]]
-[[Category: Norcoclaurine synthase]]
-[[Category: S- norcoclaurine biosynthesis]]

2vq5: Difference between revisions

Latest revision as of 01:27, 21 November 2024

X-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine and hydroxybenzaldehyde

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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