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Overview for MACiE Entry M0190

Version history

General Information

EC Number: 5.3.3.2 (A member of the Isomerases, Intramolecular oxidoreductases, Transposing C=C bonds)

Enzyme Name: isopentenyl-diphosphate delta-isomerase

Biological Species: Escherichia coli (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • Q46822 - Isopentenyl-diphosphate Delta-isomerase

Representative PDB Code: 1nfs - STRUCTURE AND MECHANISM OF ACTION OFISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATEISOMERASE: COMPLEX WITH NIPP (Resolution = 1.96 Å).

Catalytic CATH Codes:

  • 3.90.79.10 - Nucleoside Triphosphate Pyrophosphohydrolase

"Other" CATH Codes:

  • 3.90.79.10 - Nucleoside Triphosphate Pyrophosphohydrolase

Display structure information

Overall Reaction:

Image of isopentenyl diphosphate

right arrow

Image of dimethylallyl diphosphate

isopentenyl diphosphate
C00129
CHEBI:16584
dimethylallyl diphosphate
C00235
CHEBI:16057

Overall Comment: The residues that donate and abstract protons in this reaction are likely to exist as an equilibrium mixture of protonated and deprotonated forms thus they would be capable of reversing roles for isomerisation of the product of this reaction.


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Stepwise Description of the Reaction

Step 1The double bond of the isopentenyl diphosphate substrate deprotonates Tyr104.
Step 2The thiolate of Cys67 deprotonates the carbon adjacent to the newly formed carbocation, reforming the double bond in the dimethylallyl diphosphate product.
Step 3Tyr104 deprotonates water, which in turn deprotonates Cys67 in an inferred return step.

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Catalytic Residues Involved

Type Number Chain Location of Function
Cys 67 A Side Chain
Glu 116 A Side Chain
Trp 161 A Side Chain
Tyr 104 A Side Chain

Metal Cofactors for M0190

Type Het group Number Chain
manganese MN 201 A Overview
magnesium MG 401 A Overview

References

  1. V. Durbecq et al. (2001), The EMBO Journal, 20, 1530-1537. Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase.
    Medline: 11285217
  2. J. Wouters et al. (2003), J. Biol. Chem., 278, 11903-11908. 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.
    Medline: 12540835
  3. J. Wouters et al. (2003), J. Am. Chem. Soc., 125, 3198-3199. Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase.
    Medline: 12630859

Homologue information for M0190 (1nfs)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
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isopentenyl-diphosphate delta-isomerase activity (molecular function)
isoprenoid biosynthetic process (biological process)
hydrolase activity (molecular function)
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