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4f86

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Revision as of 04:40, 7 October 2022

Structure analysis of Geranyl diphosphate methyltransferase in complex with GPP and sinefungin

Structural highlights

4f86 is a 12 chain structure with sequence from Streptomyces lasalocidi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GPPMT_STRLS Catalyzes the SAM-dependent methylation of geranyl diphosphate (GPP) to yield (E)-2-methylgeranyl diphosphate (2-MeGPP).

Publication Abstract from PubMed

In the typical isoprenoid-biosynthesis pathway, condensation of the universal C(5)-unit precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) occurs via the common intermediates prenyl pyrophosphates (C(10)-C(20)). The diversity of isoprenoids reflects differences in chain length, cyclization and further additional modification after cyclization. In contrast, the biosynthesis of 2-methylisonorneol (2-MIB), which is responsible for taste and odour problems in drinking water, is unique in that it primes the enzymatic methylation of geranyl pyrophosphate (GPP) before cyclization, which is catalyzed by an S-adenosyl-L-methionine-dependent methyltransferase (GPPMT). The substrate of GPPMT contains a nonconjugated olefin and the reaction mechanism is expected to be similar to that of the steroid methyltransferase (SMT) family. Here, structural analysis of GPPMT in complex with its cofactor and substrate revealed the mechanisms of substrate recognition and possible enzymatic reaction. Using the structures of these complexes, methyl-group transfer and the subsequent proton-abstraction mechanism are discussed. GPPMT and SMTs contain a conserved glutamate residue that is likely to play a role as a general base. Comparison with the reaction mechanism of the mycolic acid cyclopropane synthase (MACS) family also supports this result. This enzyme represented here is the first model of the enzymatic C-methylation of a nonconjugated olefin in the isoprenoid-biosynthesis pathway. In addition, an elaborate system to avoid methylation of incorrect substrates is proposed.

Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependent C-methylation.,Ariyawutthiphan O, Ose T, Minami A, Sinde S, Tsuda M, Gao YG, Yao M, Oikawa H, Tanaka I Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1558-69. doi:, 10.1107/S0907444912038486. Epub 2012 Oct 18. PMID:23090405^[1]

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

References

↑ Ariyawutthiphan O, Ose T, Minami A, Sinde S, Tsuda M, Gao YG, Yao M, Oikawa H, Tanaka I. Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependent C-methylation. Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1558-69. doi:, 10.1107/S0907444912038486. Epub 2012 Oct 18. PMID:23090405 doi:10.1107/S0907444912038486

1 Structural highlights
2 Function
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/4f86"

@@ Line 1: / Line 1: @@
 ==Structure analysis of Geranyl diphosphate methyltransferase in complex with GPP and sinefungin==
-<StructureSection load='4f86' size='340' side='right' caption='[[4f86]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='4f86' size='340' side='right'caption='[[4f86]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4f86]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/'streptomyces_lasaliensis' 'streptomyces lasaliensis']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F86 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F86 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4f86]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lasalocidi Streptomyces lasalocidi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F86 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F86 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4f84|4f84]], [[4f85|4f85]]</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=4f86 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f86 OCA], [https://pdbe.org/4f86 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f86 RCSB], [https://www.ebi.ac.uk/pdbsum/4f86 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f86 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gdpmt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=324833 'Streptomyces lasaliensis'])</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=4f86 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f86 OCA], [http://pdbe.org/4f86 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f86 RCSB], [http://www.ebi.ac.uk/pdbsum/4f86 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f86 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GPPMT_STRLS GPPMT_STRLS]] Catalyzes the SAM-dependent methylation of geranyl diphosphate (GPP) to yield (E)-2-methylgeranyl diphosphate (2-MeGPP).
+[https://www.uniprot.org/uniprot/GPPMT_STRLS GPPMT_STRLS] Catalyzes the SAM-dependent methylation of geranyl diphosphate (GPP) to yield (E)-2-methylgeranyl diphosphate (2-MeGPP).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Streptomyces lasaliensis]]
+[[Category: Large Structures]]
-[[Category: Ariyawutthiphan, O]]
+[[Category: Streptomyces lasalocidi]]
-[[Category: Gao, Y G]]
+[[Category: Ariyawutthiphan O]]
-[[Category: Minami, A]]
+[[Category: Gao YG]]
-[[Category: Oikawa, H]]
+[[Category: Minami A]]
-[[Category: Ose, T]]
+[[Category: Oikawa H]]
-[[Category: Tanaka, I]]
+[[Category: Ose T]]
-[[Category: Yao, M]]
+[[Category: Tanaka I]]
-[[Category: Alpha/beta]]
+[[Category: Yao M]]
-[[Category: Methyltransferase]]
-[[Category: Rossmann fold]]
-[[Category: Transferase]]

4f86

From Proteopedia

Revision as of 04:40, 7 October 2022

Structure analysis of Geranyl diphosphate methyltransferase in complex with GPP and sinefungin

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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