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Literature summary for 5.3.3.2 extracted from

  • Durbecq, V.; Sainz, G.; Oudjama, Y.; Clantin, B.; Bompard-Gilles, C.; Tricot, C.; Caillet, J.; Stalon, V.; Droogmans, L.; Villeret, V.
    Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase (2001), EMBO J., 20, 1530-1537.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

Crystallization (Comment) Organism
crystal structure of free and metal-bound C67A mutant enzyme Escherichia coli

Protein Variants

Protein Variants Comment Organism
C67A inactive mutant enzyme Escherichia coli
E116Q the ratio of maximal velocity to turnover number is 0.09%% of that of the wild-type enzyme Escherichia coli
E87Q the ratio of maximal velocity to turnover number is 0.07% of that of the wild-type enzyme Escherichia coli
K55A the ratio of maximal velocity to turnover number is 66% of that of the wild-type enzyme Escherichia coli
K55R the ratio of maximal velocity to turnover number is 28% of that of the wild-type enzyme Escherichia coli
R51K the ratio of maximal velocity to turnover number is 4.2% of that of the wild-type enzyme Escherichia coli
R83K the ratio of maximal velocity to turnover number is 104% of that of the wild-type enzyme Escherichia coli
W161F the ratio of maximal velocity to turnover number is 0.8% of that of the wild-type enzyme Escherichia coli

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0008
-
isopentenyl diphosphate mutant enzyme W161F Escherichia coli
0.003
-
isopentenyl diphosphate mutant enzyme R83K Escherichia coli
0.0035
-
isopentenyl diphosphate wild-type enzyme Escherichia coli
0.0115
-
isopentenyl diphosphate mutant enzyme E87Q Escherichia coli
0.014
-
isopentenyl diphosphate mutant enzyme K55A Escherichia coli
0.015
-
isopentenyl diphosphate mutant enzyme K55R Escherichia coli
0.0185
-
isopentenyl diphosphate mutant enzyme R51K Escherichia coli
0.021
-
isopentenyl diphosphate mutant enzyme E116Q Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ the enzyme requires one Mn2+ or Mg2+ ion to fold in its active conformation, forming a distorted octahedral metal coordination site composed of three histidines and two glutamates and located in the active site Escherichia coli
Mn2+ the enzyme requires one Mn2+ or Mg2+ ion to fold in its active conformation, forming a distorted octahedral metal coordination site composed of three histidines and two glutamates and located in the active site Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
isopentenyl diphosphate Escherichia coli the enzyme catalyzes a crucial activation step in the isoprenoid biosynthesis pathway dimethylallyl diphosphate
-
?

Organism

Organism UniProt Comment Textmining
Escherichia coli Q46822
-
-

Purification (Commentary)

Purification (Comment) Organism
-
Escherichia coli

Reaction

Reaction Comment Organism Reaction ID
Isopentenyl diphosphate = dimethylallyl diphosphate catalytic mechanism in which a cysteine initiates the reaction by protonating the carbon-carbon double bond, with the antarafacial rearrangement ultimately achieved by one of the glutamates involved in the metal coordination sphere Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
isopentenyl diphosphate
-
Escherichia coli dimethylallyl diphosphate
-
?
isopentenyl diphosphate the enzyme catalyzes a crucial activation step in the isoprenoid biosynthesis pathway Escherichia coli dimethylallyl diphosphate
-
?

Synonyms

Synonyms Comment Organism
IPP:DMAPP
-
Escherichia coli