3vkj: Difference between revisions

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[[Image:3vkj.jpg|left|200px]]


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==Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form==
The line below this paragraph, containing "STRUCTURE_3vkj", creates the "Structure Box" on the page.
<StructureSection load='3vkj' size='340' side='right'caption='[[3vkj]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3vkj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_shibatae Saccharolobus shibatae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VKJ FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene></td></tr>
{{STRUCTURE_3vkj|  PDB=3vkj  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vkj OCA], [https://pdbe.org/3vkj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vkj RCSB], [https://www.ebi.ac.uk/pdbsum/3vkj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vkj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IDI2_SACSH IDI2_SACSH] Involved in the biosynthesis of isoprenoids. Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).[HAMAP-Rule:MF_00354]<ref>PMID:19158086</ref> <ref>PMID:22158896</ref> <ref>PMID:22505674</ref>  


===Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form===
==See Also==
 
*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
 
== References ==
==About this Structure==
<references/>
[[3vkj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_shibatae Sulfolobus shibatae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VKJ OCA].
__TOC__
[[Category: Isopentenyl-diphosphate Delta-isomerase]]
</StructureSection>
[[Category: Sulfolobus shibatae]]
[[Category: Large Structures]]
[[Category: Goda, S.]]
[[Category: Saccharolobus shibatae]]
[[Category: Hemmi, H.]]
[[Category: Goda S]]
[[Category: Nagai, T.]]
[[Category: Hemmi H]]
[[Category: Nakatani, H.]]
[[Category: Nagai T]]
[[Category: Unno, H.]]
[[Category: Nakatani H]]
[[Category: Yoshimura, T.]]
[[Category: Unno H]]
[[Category: Isomerase]]
[[Category: Yoshimura T]]
[[Category: Type 2 isopentenyl diphosphate isomerase]]

Latest revision as of 11:40, 20 March 2024

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric formCrystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form

Structural highlights

3vkj is a 4 chain structure with sequence from Saccharolobus shibatae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IDI2_SACSH Involved in the biosynthesis of isoprenoids. Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).[HAMAP-Rule:MF_00354][1] [2] [3]

See Also

References

  1. ↑ Unno H, Yamashita S, Ikeda Y, Sekiguchi SY, Yoshida N, Yoshimura T, Kusunoki M, Nakayama T, Nishino T, Hemmi H. New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase. J Biol Chem. 2009 Apr 3;284(14):9160-7. Epub 2009 Jan 21. PMID:19158086 doi:10.1074/jbc.M808438200
  2. ↑ Nagai T, Unno H, Janczak MW, Yoshimura T, Poulter CD, Hemmi H. Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors. Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20461-6. Epub 2011 Dec 7. PMID:22158896 doi:10.1073/pnas.1115749108
  3. ↑ Nakatani H, Goda S, Unno H, Nagai T, Yoshimura T, Hemmi H. Substrate-Induced Change in the Quaternary Structure of Type 2 Isopentenyl Diphosphate Isomerase from Sulfolobus shibatae. J Bacteriol. 2012 Jun;194(12):3216-24. Epub 2012 Apr 13. PMID:22505674 doi:10.1128/JB.00068-12

3vkj, resolution 1.70Å

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