3aq0: Difference between revisions

Latest revision as of 15:51, 4 October 2023

Ligand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase (surface polar residue mutant)

Structural highlights

3aq0 is a 8 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.65Å
Ligands:	FPP, ISY, MG, PEG, PPV
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SPS3_ARATH May be involved in the supply of solanesyl diphosphate for ubiquinone-9 biosynthesis in mitochondria. Synthesizes C25 to C45 medium / long-chain products depending on the type of substrate available. Can use geranyl diphosphate, farnesyl diphosphate or geranylgeranyl diphosphate as substrates, but not dimethylallyl diphosphate.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Prenyltransferases (PTSs) are involved in the biosynthesis of terpenes with diverse functions. Here a novel PTS from Arabidopsis thaliana as a trans-type polyprenyl pyrophosphate synthase (AtPPPS), which forms a trans double bond during each homoallylic substrate condensation, rather than a homomeric C(10)-geranyl pyrophosphate synthase as originally proposed. Biochemical and genetic complementation analyses indicate that AtPPPS synthesizes C(25) to C(45) medium/long-chain products. Its close relationship to other long-chain PTSs is also uncovered by phylogenetic analysis. A mutant of contiguous surface polar residues was produced by replacing four charged surface amino acids with alanines to facilitate the crystallization of the enzyme. The crystal structures of AtPPPS determined here in apo and ligand-bound forms further reveal an active-site cavity sufficient to accommodate the medium/long-chain products. The two monomers in each dimer adopt different conformations at the entrance of the active site depending on the binding of substrates. Taken together, these results suggest that AtPPPS is endowed with a unique functionality among the known PTSs.

Structure and mechanism of an Arabidopsis medium/long-chain length prenyl pyrophosphate synthase.,Hsieh FL, Chang TH, Ko TP, Wang AH Plant Physiol. 2011 Jan 10. PMID:21220764^[5]

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

References

↑ Bouvier F, Suire C, d'Harlingue A, Backhaus RA, Camara B. Molecular cloning of geranyl diphosphate synthase and compartmentation of monoterpene synthesis in plant cells. Plant J. 2000 Oct;24(2):241-52. PMID:11069698
↑ van Schie CC, Ament K, Schmidt A, Lange T, Haring MA, Schuurink RC. Geranyl diphosphate synthase is required for biosynthesis of gibberellins. Plant J. 2007 Nov;52(4):752-62. Epub 2007 Sep 18. PMID:17877699 doi:https://dx.doi.org/10.1111/j.1365-313X.2007.03273.x
↑ Ducluzeau AL, Wamboldt Y, Elowsky CG, Mackenzie SA, Schuurink RC, Basset GJ. Gene network reconstruction identifies the authentic trans-prenyl diphosphate synthase that makes the solanesyl moiety of ubiquinone-9 in Arabidopsis. Plant J. 2012 Jan;69(2):366-75. doi: 10.1111/j.1365-313X.2011.04796.x. Epub 2011 , Oct 25. PMID:21950843 doi:https://dx.doi.org/10.1111/j.1365-313X.2011.04796.x
↑ Hsieh FL, Chang TH, Ko TP, Wang AH. Structure and mechanism of an Arabidopsis medium/long-chain length prenyl pyrophosphate synthase. Plant Physiol. 2011 Jan 10. PMID:21220764 doi:10.1104/pp.110.168799
↑ Hsieh FL, Chang TH, Ko TP, Wang AH. Structure and mechanism of an Arabidopsis medium/long-chain length prenyl pyrophosphate synthase. Plant Physiol. 2011 Jan 10. PMID:21220764 doi:10.1104/pp.110.168799

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Bouvier F, Suire C, d'Harlingue A, Backhaus RA, Camara B. Molecular cloning of geranyl diphosphate synthase and compartmentation of monoterpene synthesis in plant cells. Plant J. 2000 Oct;24(2):241-52. PMID:11069698

[2] van Schie CC, Ament K, Schmidt A, Lange T, Haring MA, Schuurink RC. Geranyl diphosphate synthase is required for biosynthesis of gibberellins. Plant J. 2007 Nov;52(4):752-62. Epub 2007 Sep 18. PMID:17877699 doi:https://dx.doi.org/10.1111/j.1365-313X.2007.03273.x

[3] Ducluzeau AL, Wamboldt Y, Elowsky CG, Mackenzie SA, Schuurink RC, Basset GJ. Gene network reconstruction identifies the authentic trans-prenyl diphosphate synthase that makes the solanesyl moiety of ubiquinone-9 in Arabidopsis. Plant J. 2012 Jan;69(2):366-75. doi: 10.1111/j.1365-313X.2011.04796.x. Epub 2011 , Oct 25. PMID:21950843 doi:https://dx.doi.org/10.1111/j.1365-313X.2011.04796.x

[4] Hsieh FL, Chang TH, Ko TP, Wang AH. Structure and mechanism of an Arabidopsis medium/long-chain length prenyl pyrophosphate synthase. Plant Physiol. 2011 Jan 10. PMID:21220764 doi:10.1104/pp.110.168799

[5] Hsieh FL, Chang TH, Ko TP, Wang AH. Structure and mechanism of an Arabidopsis medium/long-chain length prenyl pyrophosphate synthase. Plant Physiol. 2011 Jan 10. PMID:21220764 doi:10.1104/pp.110.168799

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[4]

[5]

@@ Line 3: / Line 3: @@
 <StructureSection load='3aq0' size='340' side='right'caption='[[3aq0]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3aq0]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AQ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AQ0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3aq0]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AQ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AQ0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ISY:3-METHYLBUT-3-ENYLSULFANYL(PHOSPHONOOXY)PHOSPHINIC+ACID'>ISY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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]] 2.65&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3apz|3apz]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ISY:3-METHYLBUT-3-ENYLSULFANYL(PHOSPHONOOXY)PHOSPHINIC+ACID'>ISY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AtNPPPS, gpps ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Heptaprenyl_diphosphate_synthase Heptaprenyl diphosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.30 2.5.1.30] </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=3aq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aq0 OCA], [https://pdbe.org/3aq0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aq0 RCSB], [https://www.ebi.ac.uk/pdbsum/3aq0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aq0 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SPS3_ARATH SPS3_ARATH]] May be involved in the supply of solanesyl diphosphate for ubiquinone-9 biosynthesis in mitochondria. Synthesizes C25 to C45 medium / long-chain products depending on the type of substrate available. Can use geranyl diphosphate, farnesyl diphosphate or geranylgeranyl diphosphate as substrates, but not dimethylallyl diphosphate.<ref>PMID:11069698</ref> <ref>PMID:17877699</ref> <ref>PMID:21950843</ref> <ref>PMID:21220764</ref>
+[https://www.uniprot.org/uniprot/SPS3_ARATH SPS3_ARATH] May be involved in the supply of solanesyl diphosphate for ubiquinone-9 biosynthesis in mitochondria. Synthesizes C25 to C45 medium / long-chain products depending on the type of substrate available. Can use geranyl diphosphate, farnesyl diphosphate or geranylgeranyl diphosphate as substrates, but not dimethylallyl diphosphate.<ref>PMID:11069698</ref> <ref>PMID:17877699</ref> <ref>PMID:21950843</ref> <ref>PMID:21220764</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Heptaprenyl diphosphate synthase]]
 [[Category: Large Structures]]
-[[Category: Chang, T H]]
+[[Category: Chang T-H]]
-[[Category: Hsieh, F L]]
+[[Category: Hsieh F-L]]
-[[Category: Ko, T P]]
+[[Category: Ko T-P]]
-[[Category: Wang, A H.J]]
+[[Category: Wang AH-J]]
-[[Category: All alpha-helices fold]]
-[[Category: Chroloplast]]
-[[Category: Isoprenoid biosynthetic process]]
-[[Category: Prenyltransferase]]
-[[Category: Transferase]]

3aq0: Difference between revisions

Latest revision as of 15:51, 4 October 2023

Ligand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase (surface polar residue mutant)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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