This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1ubx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:45, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ubx.jpg|left|200px]]
 
-
{{Structure
+
==STRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHETASE==
-
|PDB= 1ubx |SIZE=350|CAPTION= <scene name='initialview01'>1ubx</scene>, resolution 2.5&Aring;
+
<StructureSection load='1ubx' size='340' side='right'caption='[[1ubx]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=FPP:FARNESYL DIPHOSPHATE'>FPP</scene>
+
<table><tr><td colspan='2'>[[1ubx]] 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=1UBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UBX FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Dimethylallyltranstransferase Dimethylallyltranstransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.1 2.5.1.1]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-
|GENE=
+
<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=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=1ubx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ubx OCA], [https://pdbe.org/1ubx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ubx RCSB], [https://www.ebi.ac.uk/pdbsum/1ubx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ubx ProSAT]</span></td></tr>
 +
</table>
 +
== 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.
 +
== 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/ub/1ubx_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1ubx ConSurf].
 +
<div style="clear:both"></div>
-
'''STRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHETASE'''
+
==See Also==
-
 
+
*[[Farnesyl diphosphate synthase 3D structures|Farnesyl diphosphate synthase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
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.
+
-
 
+
-
==About this Structure==
+
-
1UBX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UBX OCA].
+
-
 
+
-
==Reference==
+
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/8986756 8986756]
+
-
[[Category: Dimethylallyltranstransferase]]
+
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
-
[[Category: Single protein]]
+
[[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: FPP]]
+
-
[[Category: MG]]
+
-
[[Category: cholesterol biosynthesis]]
+
-
[[Category: isoprene biosynthesis]]
+
-
[[Category: transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:29:58 2008''
+

Current revision

STRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHETASE

PDB ID 1ubx

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ubx"
Personal tools