3vc1

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Current revision (10:35, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3vc1' size='340' side='right'caption='[[3vc1]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
<StructureSection load='3vc1' size='340' side='right'caption='[[3vc1]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vc1]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VC1 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vc1]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VC1 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GST:GERANYL+S-THIOLODIPHOSPHATE'>GST</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.82&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vc2|3vc2]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GST:GERANYL+S-THIOLODIPHOSPHATE'>GST</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">orf4, SCBAC12C8.02, SCO7701 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vc1 OCA], [https://pdbe.org/3vc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vc1 RCSB], [https://www.ebi.ac.uk/pdbsum/3vc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vc1 ProSAT]</span></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=3vc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vc1 OCA], [https://pdbe.org/3vc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vc1 RCSB], [https://www.ebi.ac.uk/pdbsum/3vc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vc1 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/GPPMT_STRCO GPPMT_STRCO]] Catalyzes the SAM-dependent methylation of geranyl diphosphate (GPP) to yield (E)-2-methylgeranyl diphosphate (2-MeGPP).<ref>PMID:18563898</ref>
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[https://www.uniprot.org/uniprot/GPPMT_STRCO GPPMT_STRCO] Catalyzes the SAM-dependent methylation of geranyl diphosphate (GPP) to yield (E)-2-methylgeranyl diphosphate (2-MeGPP).<ref>PMID:18563898</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Geranyl diphosphate C-methyltransferase (GPPMT) from Streptomyces coelicolor A3(2) is the first methyltransferase discovered that modifies an acyclic isoprenoid diphosphate, geranyl diphosphate (GPP), to yield a noncanonical acyclic allylic diphosphate product, 2-methylgeranyl diphosphate, which serves as the substrate for a subsequent cyclization reaction catalyzed by a terpenoid cyclase, methylisoborneol synthase. Here, we report the crystal structures of GPPMT in complex with GPP or the substrate analogue geranyl S-thiolodiphosphate (GSPP) along with S-adenosyl-l-homocysteine in the cofactor binding site, resulting from in situ demethylation of S-adenosyl-l-methionine, at 2.05 or 1.82 A resolution, respectively. These structures suggest that both GPP and GSPP can undergo catalytic methylation in crystalline GPPMT, followed by dissociation of the isoprenoid product. S-Adenosyl-l-homocysteine remains bound in the active site, however, and does not exchange with a fresh molecule of cofactor S-adenosyl-l-methionine. These structures provide important clues about the molecular mechanism of the reaction, especially with regard to the face of the 2,3 double bond of GPP that is methylated as well as the stabilization of the resulting carbocation intermediate through cation-pi interactions.
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Structure of Geranyl Diphosphate C-Methyltransferase from Streptomyces coelicolor and Implications for the Mechanism of Isoprenoid Modification.,Koksal M, Chou WK, Cane DE, Christianson DW Biochemistry. 2012 Apr 10;51(14):3003-10. Epub 2012 Mar 28. PMID:22455498<ref>PMID:22455498</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3vc1" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Strco]]
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[[Category: Christianson DW]]
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[[Category: Christianson, D W]]
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[[Category: Koksal M]]
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[[Category: Koksal, M]]
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[[Category: 2-methylisoborneol biosynthesis]]
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[[Category: C-methyltransferase]]
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[[Category: Methyltransferase fold]]
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[[Category: Rossmann fold]]
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[[Category: Sam-dependent methyltransferase]]
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[[Category: Terpenoid biosynthesis]]
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[[Category: Transferase]]
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Current revision

Crystal structure of geranyl diphosphate C-methyltransferase from Streptomyces coelicolor A3(2) in complex with Mg2+, geranyl-S-thiolodiphosphate, and S-adenosyl-L-homocysteine

PDB ID 3vc1

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OCA

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