2zrv: Difference between revisions

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<StructureSection load='2zrv' size='340' side='right'caption='[[2zrv]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='2zrv' size='340' side='right'caption='[[2zrv]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2zrv]] 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=2ZRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZRV FirstGlance]. <br>
<table><tr><td colspan='2'>[[2zrv]] 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=2ZRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZRV 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]] 2.3&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zru|2zru]], [[2zrw|2zrw]], [[2zrx|2zrx]], [[2zry|2zry]], [[2zrz|2zrz]]</div></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='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 'Saccharolobus shibatae'])</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=2zrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zrv OCA], [https://pdbe.org/2zrv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zrv RCSB], [https://www.ebi.ac.uk/pdbsum/2zrv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zrv 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=2zrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zrv OCA], [https://pdbe.org/2zrv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zrv RCSB], [https://www.ebi.ac.uk/pdbsum/2zrv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zrv 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>
== 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=2zrv 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=2zrv ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Using FMN and a reducing agent such as NAD(P)H, type 2 isopentenyl-diphosphate isomerase catalyzes isomerization between isopentenyl diphosphate and dimethylallyl diphosphate, both of which are elemental units for the biosynthesis of highly diverse isoprenoid compounds. Although the flavin cofactor is expected to be integrally involved in catalysis, its exact role remains controversial. Here we report the crystal structures of the substrate-free and complex forms of type 2 isopentenyl-diphosphate isomerase from the thermoacidophilic archaeon Sulfolobus shibatae, not only in the oxidized state but also in the reduced state. Based on the active-site structures of the reduced FMN-substrate-enzyme ternary complexes, which are in the active state, and on the data from site-directed mutagenesis at highly conserved charged or polar amino acid residues around the active site, we demonstrate that only reduced FMN, not amino acid residues, can catalyze proton addition/elimination required for the isomerase reaction. This discovery is the first evidence for this long suspected, but previously unobserved, role of flavins just as a general acid-base catalyst without playing any redox roles, and thereby expands the known functions of these versatile coenzymes.
New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.,Unno H, Yamashita S, Ikeda Y, Sekiguchi SY, Yoshida N, Yoshimura T, Kusunoki M, Nakayama T, Nishino T, Hemmi H J Biol Chem. 2009 Apr 3;284(14):9160-7. Epub 2009 Jan 21. PMID:19158086<ref>PMID:19158086</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2zrv" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharolobus shibatae]]
[[Category: Saccharolobus shibatae]]
[[Category: Isopentenyl-diphosphate Delta-isomerase]]
[[Category: Hemmi H]]
[[Category: Large Structures]]
[[Category: Ikeda Y]]
[[Category: Hemmi, H]]
[[Category: Kusunoki M]]
[[Category: Ikeda, Y]]
[[Category: Nakayama T]]
[[Category: Kusunoki, M]]
[[Category: Nishino T]]
[[Category: Nakayama, T]]
[[Category: Sekiguchi S]]
[[Category: Nishino, T]]
[[Category: Unno H]]
[[Category: Sekiguchi, S]]
[[Category: Yamashita S]]
[[Category: Unno, H]]
[[Category: Yoshida N]]
[[Category: Yamashita, S]]
[[Category: Yoshimura T]]
[[Category: Yoshida, N]]
[[Category: Yoshimura, T]]
[[Category: Flavoprotein]]
[[Category: Fmn]]
[[Category: Idi]]
[[Category: Isomerase]]
[[Category: Isopentenyl diphosphate isomerase]]
[[Category: Isoprene biosynthesis]]
[[Category: Nadp]]
[[Category: Reduced form]]
[[Category: Type 2]]

Latest revision as of 16:58, 13 March 2024

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN.Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN.

Structural highlights

2zrv 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 2.3Å
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]

Evolutionary Conservation

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

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

2zrv, resolution 2.30Å

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