3vkj: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='3vkj' size='340' side='right'caption='[[3vkj]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='3vkj' size='340' side='right'caption='[[3vkj]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3vkj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_51178 Atcc 51178]. 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>
<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>
</td></tr><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>
</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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fni, idi ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2286 ATCC 51178])</td></tr>
<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>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Isopentenyl-diphosphate_Delta-isomerase Isopentenyl-diphosphate Delta-isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.2 5.3.3.2] </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=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>
<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>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/IDI2_SULSH IDI2_SULSH]] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity).  
[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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Type 2 isopentenyl diphosphate isomerase catalyzes the interconversion between two active units for isoprenoid biosynthesis, i.e., isopentenyl diphosphate and dimethylallyl diphosphate, in almost all archaea and in some bacteria, including human pathogens. The enzyme is a good target for discovery of antibiotics because it is essential for the organisms that use only the mevalonate pathway to produce the active isoprene units and because humans possess a nonhomologous isozyme, type 1 isopentenyl diphosphate isomerase. However, type 2 enzymes were reportedly inhibited by mechanism-based drugs for the type 1 enzyme due to their surprisingly similar reaction mechanisms. Thus, a different approach is now required to develop new inhibitors specific to the type 2 enzyme. X-ray crystallography and gel filtration chromatography revealed that the enzyme from a thermoacidophilic archaeon, Sulfolobus shibatae, is in the octameric state at a high concentration. Interestingly, a part of the regions that are involved in the substrate binding in the previously reported tetrameric structures is integral to the formation of the tetramer-tetramer interface in the substrate-free octameric structure. Site-directed mutagenesis at such regions resulted in stabilization of the tetramer. Small-angle X-ray scattering, tryptophan fluorescence, and dynamic light scattering analyses showed that substrate binding causes the dissociation of an octamer into tetramers. This property, i.e., incompatibility between octamer formation and substrate binding, might provide clues to develop new specific inhibitors of the archaeal enzyme.
 
Substrate-Induced Change in the Quaternary Structure of Type 2 Isopentenyl Diphosphate Isomerase from Sulfolobus shibatae.,Nakatani H, Goda S, Unno H, Nagai T, Yoshimura T, Hemmi H J Bacteriol. 2012 Jun;194(12):3216-24. Epub 2012 Apr 13. PMID:22505674<ref>PMID:22505674</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3vkj" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
Line 27: Line 17:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 51178]]
[[Category: Isopentenyl-diphosphate Delta-isomerase]]
[[Category: Large Structures]]
[[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

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=3vkj&oldid=4104387"