1nfs: Difference between revisions

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New page: left|200px<br /><applet load="1nfs" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nfs, resolution 1.96Å" /> '''STRUCTURE AND MECHAN...
 
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'''STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPP'''<br />


==Overview==
==STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPP==
Isopentenyl diphosphate (IPP):dimethylallyl diphosphate (DMAPP) isomerase, is a key enzyme in the biosynthesis of isoprenoids. The reaction involves, protonation and deprotonation of the isoprenoid unit and proceeds through, a carbocationic transition state. Analysis of the crystal structures (2 A), of complexes of Escherichia coli IPP.DMAPPs isomerase with a transition, state analogue (N,N-dimethyl-2-amino-1-ethyl diphosphate) and a covalently, attached irreversible inhibitor (3,4-epoxy-3-methyl-1-butyl diphosphate), indicates that Glu-116, Tyr-104, and Cys-67 are involved in the, antarafacial addition/elimination of protons during isomerization. This, work provides a new perspective about the mechanism of the reaction.
<StructureSection load='1nfs' size='340' side='right'caption='[[1nfs]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1nfs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NFS FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DED:2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE'>DED</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=1nfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nfs OCA], [https://pdbe.org/1nfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nfs RCSB], [https://www.ebi.ac.uk/pdbsum/1nfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nfs ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IDI_ECOLI IDI_ECOLI] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).<ref>PMID:10099534</ref> <ref>PMID:9603997</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/nf/1nfs_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1nfs ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Isopentenyl diphosphate (IPP):dimethylallyl diphosphate (DMAPP) isomerase is a key enzyme in the biosynthesis of isoprenoids. The reaction involves protonation and deprotonation of the isoprenoid unit and proceeds through a carbocationic transition state. Analysis of the crystal structures (2 A) of complexes of Escherichia coli IPP.DMAPPs isomerase with a transition state analogue (N,N-dimethyl-2-amino-1-ethyl diphosphate) and a covalently attached irreversible inhibitor (3,4-epoxy-3-methyl-1-butyl diphosphate) indicates that Glu-116, Tyr-104, and Cys-67 are involved in the antarafacial addition/elimination of protons during isomerization. This work provides a new perspective about the mechanism of the reaction.


==About this Structure==
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.,Wouters J, Oudjama Y, Barkley SJ, Tricot C, Stalon V, Droogmans L, Poulter CD J Biol Chem. 2003 Apr 4;278(14):11903-8. Epub 2003 Jan 22. PMID:12540835<ref>PMID:12540835</ref>
1NFS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MN, MG and DED as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Isopentenyl-diphosphate_Delta-isomerase Isopentenyl-diphosphate Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.2 5.3.3.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NFS OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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., Wouters J, Oudjama Y, Barkley SJ, Tricot C, Stalon V, Droogmans L, Poulter CD, J Biol Chem. 2003 Apr 4;278(14):11903-8. Epub 2003 Jan 22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12540835 12540835]
</div>
<div class="pdbe-citations 1nfs" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Isopentenyl-diphosphate Delta-isomerase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Wouters J]]
[[Category: Wouters, J.]]
[[Category: DED]]
[[Category: MG]]
[[Category: MN]]
[[Category: complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:13:15 2007''

Latest revision as of 12:19, 16 August 2023

STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPPSTRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPP

Structural highlights

1nfs is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.96Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IDI_ECOLI Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).[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

Isopentenyl diphosphate (IPP):dimethylallyl diphosphate (DMAPP) isomerase is a key enzyme in the biosynthesis of isoprenoids. The reaction involves protonation and deprotonation of the isoprenoid unit and proceeds through a carbocationic transition state. Analysis of the crystal structures (2 A) of complexes of Escherichia coli IPP.DMAPPs isomerase with a transition state analogue (N,N-dimethyl-2-amino-1-ethyl diphosphate) and a covalently attached irreversible inhibitor (3,4-epoxy-3-methyl-1-butyl diphosphate) indicates that Glu-116, Tyr-104, and Cys-67 are involved in the antarafacial addition/elimination of protons during isomerization. This work provides a new perspective about the mechanism of the reaction.

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.,Wouters J, Oudjama Y, Barkley SJ, Tricot C, Stalon V, Droogmans L, Poulter CD J Biol Chem. 2003 Apr 4;278(14):11903-8. Epub 2003 Jan 22. PMID:12540835[3]

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

See Also

References

  1. ↑ Wang CW, Oh MK, Liao JC. Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli. Biotechnol Bioeng. 1999 Jan 20;62(2):235-41. PMID:10099534
  2. ↑ Hemmi H, Ohnuma S, Nagaoka K, Nishino T. Identification of genes affecting lycopene formation in Escherichia coli transformed with carotenoid biosynthetic genes: candidates for early genes in isoprenoid biosynthesis. J Biochem. 1998 Jun;123(6):1088-96. PMID:9603997
  3. ↑ 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

1nfs, resolution 1.96Å

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