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2z78

From Proteopedia

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S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with BPH-806

Structural highlights

2z78 is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GGPPS_YEAST Catalyzes the trans-addition of the 3 molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate. Required for the membrane attachment of YPT1 and SEC4. May be involved in vesicle trafficking and protein sorting.^[1] ^[2]

Evolutionary Conservation

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

Publication Abstract from PubMed

We report the X-ray structures of several bisphosphonate inhibitors of geranylgeranyl diphosphate synthase, a target for anticancer drugs. Bisphosphonates containing unbranched side chains bind to either the farnesyl diphosphate (FPP) substrate site, the geranylgeranyl diphosphate (GGPP) product site, and in one case, both sites, with the bisphosphonate moiety interacting with 3 Mg (2+) that occupy the same position as found in FPP synthase. However, each of three "V-shaped" bisphosphonates bind to both the FPP and GGPP sites. Using the Glide program, we reproduced the binding modes of 10 bisphosphonates with an rms error of 1.3 A. Activities of the bisphosphonates in GGPPS inhibition were predicted with an overall error of 2x by using a comparative molecular similarity analysis based on a docked-structure alignment. These results show that some GGPPS inhibitors can occupy both substrate and product site and that binding modes as well as activity can be accurately predicted, facilitating the further development of GGPPS inhibitors as anticancer agents.

Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation.,K-M Chen C, Hudock MP, Zhang Y, Guo RT, Cao R, No JH, Liang PH, Ko TP, Chang TH, Chang SC, Song Y, Axelson J, Kumar A, Wang AH, Oldfield E J Med Chem. 2008 Sep 25;51(18):5594-607. PMID:18800762^[3]

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

References

↑ Jiang Y, Proteau P, Poulter D, Ferro-Novick S. BTS1 encodes a geranylgeranyl diphosphate synthase in Saccharomyces cerevisiae. J Biol Chem. 1995 Sep 15;270(37):21793-9. PMID:7665600
↑ Shiflett SL, Vaughn MB, Huynh D, Kaplan J, Ward DM. Bph1p, the Saccharomyces cerevisiae homologue of CHS1/beige, functions in cell wall formation and protein sorting. Traffic. 2004 Sep;5(9):700-10. PMID:15296494 doi:http://dx.doi.org/10.1111/j.1600-0854.2004.00213.x
↑ K-M Chen C, Hudock MP, Zhang Y, Guo RT, Cao R, No JH, Liang PH, Ko TP, Chang TH, Chang SC, Song Y, Axelson J, Kumar A, Wang AH, Oldfield E. Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation. J Med Chem. 2008 Sep 25;51(18):5594-607. PMID:18800762 doi:10.1021/jm800325y

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2z78"

@@ Line 1: / Line 1: @@
 ==S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with BPH-806==
-<StructureSection load='2z78' size='340' side='right' caption='[[2z78]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2z78' size='340' side='right'caption='[[2z78]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2z78]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z78 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z78 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2z78]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z78 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z78 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H86:3-(DECYLOXY)-5-(3,5-DIFLUOROPHENYL)-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM'>H86</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]] 2.1&#8491;</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=2z78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z78 OCA], [http://pdbe.org/2z78 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z78 RCSB], [http://www.ebi.ac.uk/pdbsum/2z78 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z78 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H86:3-(DECYLOXY)-5-(3,5-DIFLUOROPHENYL)-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM'>H86</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=2z78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z78 OCA], [https://pdbe.org/2z78 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z78 RCSB], [https://www.ebi.ac.uk/pdbsum/2z78 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z78 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GGPPS_YEAST GGPPS_YEAST]] Catalyzes the trans-addition of the 3 molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate. Required for the membrane attachment of YPT1 and SEC4. May be involved in vesicle trafficking and protein sorting.<ref>PMID:7665600</ref> <ref>PMID:15296494</ref>
+[https://www.uniprot.org/uniprot/GGPPS_YEAST GGPPS_YEAST] Catalyzes the trans-addition of the 3 molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate. Required for the membrane attachment of YPT1 and SEC4. May be involved in vesicle trafficking and protein sorting.<ref>PMID:7665600</ref> <ref>PMID:15296494</ref>
 == 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/z7/2z78_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z78_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 31: @@
 ==See Also==
-*[[Geranylgeranyl pyrophosphate synthase|Geranylgeranyl pyrophosphate synthase]]
+*[[Geranylgeranyl pyrophosphate synthase 3D structures|Geranylgeranyl pyrophosphate synthase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Cao, R]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Chen, C K.M]]
+[[Category: Cao R]]
-[[Category: Guo, R T]]
+[[Category: Chen CK-M]]
-[[Category: Hudock, M]]
+[[Category: Guo RT]]
-[[Category: Oldfield, E]]
+[[Category: Hudock M]]
-[[Category: Wang, A H.J]]
+[[Category: Oldfield E]]
-[[Category: Bisphosphonate]]
+[[Category: Wang AH-J]]
-[[Category: Carotenoid biosynthesis]]
-[[Category: Geranylgeranyl pyrophosphate]]
-[[Category: Isoprene biosynthesis]]
-[[Category: Multifunctional enzyme]]
-[[Category: Prenyltransferase]]
-[[Category: Protein transport]]
-[[Category: Transferase]]
-[[Category: Transferase-transferase inhibitor complex]]
-[[Category: Transport]]

2z78

From Proteopedia

Current revision

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with BPH-806

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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