Isopentenyl-diphosphate delta-isomerase

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<StructureSection load='2zry' size='340' side='right' caption='Structure of isopentenyl-diphosphate delta-isomerase complex with FMN, Mg+2 ion (green) and IPP (PDB code [[2zry]]).' scene=''>
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<StructureSection load='1nfz' size='350' side='right' caption='Structure of E. coli isopentenyl-diphosphate delta-isomerase complex with EIPP, Mg+2 (green) and Mn+2 (purple) ions and EIPP (PDB code [[1nfz]]).' scene='59/595218/Cv/1'>
== Function ==
== Function ==
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'''Isopentenyl-diphosphate delta-isomerase''' (IPPI) catalyzes the conversion of the un-reactive isopentenyl diphosphate (IPP) to the more reactive dimethylallyl diphosphate (DMAPP). 3,4-epoxy-3-methyl butyl diphosphate (EIPP) is an irreversible inhibitor of IPPI. IPPI participates in isoprenoid biosynthesis.
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'''Isopentenyl-diphosphate delta-isomerase''' (IPPI) catalyzes the conversion of the un-reactive isopentenyl diphosphate (IPP) to the more reactive dimethylallyl diphosphate (DMAPP). 3,4-epoxy-3-methyl butyl diphosphate (EIPP) is an irreversible inhibitor of IPPI. IPPI participates in isoprenoid biosynthesis<ref>PMID:3022798</ref>.
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== Disease ==
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See also [[Mevalonate pathway]]
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== Relevance ==
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== Structural highlights ==
== Structural highlights ==
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''E. coli'' IPPI contains <scene name='59/595218/Cv/8'>2 divalent ions which interact with the irreversible inhibitor EIPP</scene><ref>PMID:12540835</ref>. Water molecules shown as red spheres.
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<scene name='59/595218/Cv/9'>Mg coordination site</scene>.
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<scene name='59/595218/Cv/10'>Mn coordination site</scene>.
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</StructureSection>
==3D structures of isopentenyl-diphosphate delta-isomerase==
==3D structures of isopentenyl-diphosphate delta-isomerase==
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*Isopentenyl-diphosphate delta-isomerase
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[[1i9a]], [[2vnq]] – EcIPPI + Mn – ''Escherichia coli''<br />
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**[[2icj]] – hIPPI + Mg - human<br />
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[[1hx3]] – EcIPPI (mutant) + Mn<br />
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**[[2dho]] – hIPPI 1 (mutant) + Mn <br />
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[[1r67]] – EcIPPI (mutant) + Mg<br />
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**[[1i9a]], [[2vnq]] – EcIPPI + Mn – ''Escherichia coli''<br />
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[[2g74]] – EcIPPI (mutant) + Mg + Mn<br />
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**[[1hx3]] – EcIPPI (mutant) + Mn<br />
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[[1hzt]] – EcIPPI <br />
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**[[1r67]] – EcIPPI (mutant) + Mg<br />
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[[1p0k]] – BsIPPI – ''Bacillus subtilis''<br />
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**[[2g74]] – EcIPPI (mutant) + Mg + Mn<br />
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[[1p0n]] – BsIPPI + FMN<br />
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**[[1hzt]] – EcIPPI <br />
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[[1vcf]] – TtIPPI + FMN + Cd – ''Thermus thermophilus''<br />
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**[[1p0k]] – BsIPPI – ''Bacillus subtilis''<br />
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[[1vcg]] – TtIPPI + FMN<br />
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**[[1p0n]] – BsIPPI + FMN<br />
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[[2zru]], [[2zrv]], [[3vkj]] – SsIPPI + FMN – ''Sulfolobus shibatae''<br />
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**[[1vcf]] – TtIPPI + FMN + Cd – ''Thermus thermophilus''<br />
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[[3hyq]] – IPPI – ''Salmonella enterica''<br />
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**[[1vcg]] – TtIPPI + FMN<br />
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[[3sr7]] – IPPI – ''Streptococcus mutans''<br />
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**[[2zru]], [[2zrv]], [[3vkj]] – SsIPPI + FMN – ''Sulfolobus shibatae''<br />
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[[4n02]] – IPPI + FMN – ''Streptococcus pneumoniae''<br />
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**[[3hyq]] – IPPI – ''Salmonella enterica''<br />
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**[[3sr7]] – IPPI – ''Streptococcus mutans''<br />
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**[[4n02]] – IPPI + FMN – ''Streptococcus pneumoniae''<br />
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===Isopentenyl-diphosphate delta-isomerase complex===
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*Isopentenyl-diphosphate delta-isomerase complex
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[[1nfs]], [[2vnp]] – EcIPPI + Mn + Mg + dimethylamino-ethyl diphosphate<br />
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**[[2i6k]] – hIPPI (mutant) + Mn + Mg + aminoethanol-PP<br />
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[[1pvf]] – EcIPPI + Mn + Mg + diphosphate<br />
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**[[2ick]] – hIPPI + Mn + dimethylallyl-PP<br />
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[[1nfz]], [[1ppw]], [[1x84]] – EcIPPI + Mn + Mg + EIPP<br />
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**[[2pny]] – hIPPI 2 + Mn + PP<br />
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[[1ow2]], [[1x83]], [[2g73]], [[2b2k]] – EcIPPI (mutant) + Mn + Mg + EIPP<br />
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**[[1nfs]], [[2vnp]] – EcIPPI + Mn + Mg + dimethylamino-ethyl-PP<br />
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[[1ppv]] – EcIPPI + Mn + Mg + bromo-EIPP<br />
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**[[1pvf]] – EcIPPI + Mn + Mg + PP<br />
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[[1q54]] – EcIPPI (mutant) + Mn + Mg + bromo-EIPP<br />
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**[[1nfz]], [[1ppw]], [[1x84]] – EcIPPI + Mn + Mg + EIPP<br />
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[[3dh7]] – TtIPPI + FMN + diphosphate<br />
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**[[1ow2]], [[1x83]], [[2g73]], [[2b2k]] – EcIPPI (mutant) + Mn + Mg + EIPP<br />
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[[3b05]], [[2zrw]], [[2zry]] – SsIPPI + FMN + Mg + IPP<br />
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**[[1ppv]] – EcIPPI + Mn + Mg + bromo-EIPP<br />
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[[3b06]], [[2zrx]], [[2zrz]] – SsIPPI + FMN + Mg + DMAPP<br />
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**[[1q54]] – EcIPPI (mutant) + Mn + Mg + bromo-EIPP<br />
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[[3b03]], [[3b04]] – SsIPPI + Mg + inhibitor<br />
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**[[3dh7]] – TtIPPI + FMN + PP<br />
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**[[3b05]], [[2zrw]], [[2zry]] – SsIPPI + FMN + Mg + IPP<br />
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**[[3b06]], [[2zrx]], [[2zrz]] – SsIPPI + FMN + Mg + DMAPP<br />
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**[[3b03]], [[3b04]] – SsIPPI + Mg + inhibitor<br />
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}}
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Structure of E. coli isopentenyl-diphosphate delta-isomerase complex with EIPP, Mg+2 (green) and Mn+2 (purple) ions and EIPP (PDB code 1nfz).

Drag the structure with the mouse to rotate

3D structures of isopentenyl-diphosphate delta-isomerase

Updated on 16-January-2023

References

  1. ↑ Reardon JE, Abeles RH. Mechanism of action of isopentenyl pyrophosphate isomerase: evidence for a carbonium ion intermediate. Biochemistry. 1986 Sep 23;25(19):5609-16. PMID:3022798
  2. ↑ Wouters J, Oudjama Y, Barkley SJ, Tricot C, Stalon V, Droogmans L, Poulter CD. Catalytic mechanism of Escherichia coli isopentenyl diphosphate isomerase involves Cys-67, Glu-116, and Tyr-104 as suggested by crystal structures of complexes with transition state analogues and irreversible inhibitors. J Biol Chem. 2003 Apr 4;278(14):11903-8. Epub 2003 Jan 22. PMID:12540835 doi:http://dx.doi.org/10.1074/jbc.M212823200

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky

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