1uby: Difference between revisions

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<StructureSection load='1uby' size='340' side='right'caption='[[1uby]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='1uby' size='340' side='right'caption='[[1uby]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1uby]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UBY FirstGlance]. <br>
<table><tr><td colspan='2'>[[1uby]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UBY FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMA:DIMETHYLALLYL+DIPHOSPHATE'>DMA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.4&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dimethylallyltranstransferase Dimethylallyltranstransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.1 2.5.1.1] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMA:DIMETHYLALLYL+DIPHOSPHATE'>DMA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1uby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uby OCA], [https://pdbe.org/1uby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uby RCSB], [https://www.ebi.ac.uk/pdbsum/1uby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uby 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=1uby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uby OCA], [https://pdbe.org/1uby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uby RCSB], [https://www.ebi.ac.uk/pdbsum/1uby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uby ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/FPPS_CHICK FPPS_CHICK]] Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.  
[https://www.uniprot.org/uniprot/FPPS_CHICK FPPS_CHICK] Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1uby ConSurf].
</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=1uby ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
An analysis of the x-ray structure of homodimeric avian farnesyl diphosphate synthase (geranyltransferase, EC 2.5.1.10) coupled with information about conserved amino acids obtained from a sequence alignment of 35 isoprenyl diphosphate synthases that synthesize farnesyl (C15), geranylgeranyl (C20), and higher chain length isoprenoid diphosphates suggested that the side chains of residues corresponding to F112 and F113 in the avian enzyme were important for determining the ultimate length of the hydrocarbon chains. This hypothesis was supported by site-directed mutagenesis to transform wild-type avian farnesyl diphosphate synthase (FPS) into synthases capable of producing geranylgeranyl diphosphate (F112A), geranylfarnesyl (C25) diphosphate (F113S), and longer chain prenyl diphosphates (F112A/F113S). An x-ray analysis of the structure of the F112A/F113S mutant in the apo state and with allylic substrates bound produced the strongest evidence that these mutations caused the observed change in product specificity by directly altering the size of the binding pocket for the growing isoprenoid chain in the active site of the enzyme. The proposed binding pocket in the apo mutant structure was increased in depth by 5.8 A as compared with that for the wild-type enzyme. Allylic diphosphates were observed in the holo structures, bound through magnesium ions to the aspartates of the first of two conserved aspartate-rich sequences (D117-D121), with the hydrocarbon tails of all the ligands growing down the hydrophobic pocket toward the mutation site. A model was constructed to show how the growth of a long chain prenyl product may proceed by creation of a hydrophobic passageway from the FPS active site to the outside surface of the enzyme.
Regulation of product chain length by isoprenyl diphosphate synthases.,Tarshis LC, Proteau PJ, Kellogg BA, Sacchettini JC, Poulter CD Proc Natl Acad Sci U S A. 1996 Dec 24;93(26):15018-23. PMID:8986756<ref>PMID:8986756</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1uby" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Farnesyl diphosphate synthase 3D structures|Farnesyl diphosphate synthase 3D structures]]
*[[Farnesyl diphosphate synthase 3D structures|Farnesyl diphosphate synthase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Chick]]
[[Category: Gallus gallus]]
[[Category: Dimethylallyltranstransferase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Poulter, C D]]
[[Category: Poulter CD]]
[[Category: Proteau, P]]
[[Category: Proteau P]]
[[Category: Sacchettini, J C]]
[[Category: Sacchettini JC]]
[[Category: Tarshis, L C]]
[[Category: Tarshis LC]]
[[Category: Cholesterol biosynthesis]]
[[Category: Isoprene biosynthesis]]
[[Category: Transferase]]

Latest revision as of 11:45, 14 February 2024

STRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHETASESTRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHETASE

Structural highlights

1uby is a 1 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FPPS_CHICK Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1uby, resolution 2.40Å

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