Literature summary extracted from
Benach, J.; Lee, I.; Edstrom, W.; Kuzin, A.P.; Chiang, Y.; Acton, T.B.; Montelione, G.T.; Hunt, J.F.
The 2.3-Å crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase (2003), J. Biol. Chem., 278, 19176-19182.
Application
EC Number |
Application |
Comment |
Organism |
---|
1.1.1.282 |
pharmacology |
enzymes of the shikimate pathway has been promoted as a target for the development of antimicrobial agents |
Escherichia coli |
Cloned(Commentary)
EC Number |
Cloned (Comment) |
Organism |
---|
1.1.1.282 |
ydiB gene, expression in Escherichia coli BL21(DE3) |
Escherichia coli |
Natural Substrates/ Products (Substrates)
EC Number |
Natural Substrates |
Organism |
Comment (Nat. Sub.) |
Natural Products |
Comment (Nat. Pro.) |
Rev. |
Reac. |
---|
1.1.1.282 |
3-dehydroshikimate + NAD(P)H + H+ |
Escherichia coli |
YdiB catalyzes the reduction of 3-dehydroshikimate to shikimate as part of the shikimate pathway |
shikimate + NAD(P)+ |
- |
? |
|
Organism
EC Number |
Organism |
UniProt |
Comment |
Textmining |
---|
1.1.1.282 |
Escherichia coli |
P0A6D5 |
- |
- |
Purification (Commentary)
EC Number |
Purification (Comment) |
Organism |
---|
1.1.1.282 |
- |
Escherichia coli |
Reaction
EC Number |
Reaction |
Comment |
Organism |
Reaction ID |
---|
1.1.1.282 |
L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+ |
reaction mechanism, in which an aspartate acts as the general acid/base catalyst during the hydride transfer |
Escherichia coli |
|
1.1.1.282 |
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+ |
reaction mechanism, in which an aspartate acts as the general acid/base catalyst during the hydride transfer |
Escherichia coli |
|
Substrates and Products (Substrate)
EC Number |
Substrates |
Comment Substrates |
Organism |
Products |
Comment (Products) |
Rev. |
Reac. |
---|
1.1.1.282 |
3-dehydroshikimate + NAD(P)H + H+ |
YdiB catalyzes the reduction of 3-dehydroshikimate to shikimate as part of the shikimate pathway |
Escherichia coli |
shikimate + NAD(P)+ |
- |
? |
|
1.1.1.282 |
L-quinate + NAD(P)+ |
detailed strucure of YdiB, specificity for binding NAD+/NADH over NADP+/NADPH |
Escherichia coli |
3-dehydroquinate + NAD(P)H + H+ |
- |
r |
|
1.1.1.282 |
shikimate + NAD(P)+ |
detailed strucure of YdiB, catalytic mechanism, specificity for binding NAD+/NADH over NADP+/NADPH |
Escherichia coli |
3-dehydroshikimate + NAD(P)H + H+ |
- |
r |
|
Subunits
EC Number |
Subunits |
Comment |
Organism |
---|
1.1.1.282 |
homodimer |
- |
Escherichia coli |
Synonyms
EC Number |
Synonyms |
Comment |
Organism |
---|
1.1.1.282 |
More |
YdiB is a class A NAD(P)+-dependent oxidoreductase |
Escherichia coli |
Temperature Optimum [°C]
EC Number |
Temperature Optimum [°C] |
Temperature Optimum Maximum [°C] |
Comment |
Organism |
---|
1.1.1.282 |
25 |
- |
assay at |
Escherichia coli |
pH Optimum
EC Number |
pH Optimum Minimum |
pH Optimum Maximum |
Comment |
Organism |
---|
1.1.1.282 |
10.6 |
- |
assay at |
Escherichia coli |
Cofactor
EC Number |
Cofactor |
Comment |
Organism |
Structure |
---|
1.1.1.282 |
NAD+ |
NAD+ binding site, bound very tightly, NAD+ is bound to the Rossmann domain in an elongated fashion with the nicotinamide ring in the pro-R conformation, specificity for binding NAD+ over NADP+ |
Escherichia coli |
|
1.1.1.282 |
NADH |
specificity for binding NADH over NADPH |
Escherichia coli |
|
1.1.1.282 |
NADP+ |
specificity for binding NAD+ over NADP+ |
Escherichia coli |
|
1.1.1.282 |
NADPH |
specificity for binding NADH over NADPH |
Escherichia coli |
|