Literature summary for 1.1.1.25 extracted from

Han, C.; Hu, T.; Wu, D.; Qu, S.; Zhou, J.; Ding, J.; Shen, X.; Qu, D.; Jiang, H.
X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis (2009), FEBS J., 276, 1125-1139.

Cloned(Commentary)

Cloned (Comment)	Organism
wild-type and mutant cloned into vector pET22b and transformed into Escherichia coli strain BL21(DE3). Selenomethionine-substituted SDH generated in the methionine auxotrophic Escherichia coli strain B834(DE3)	Staphylococcus epidermidis RP62A

Crystallization (Commentary)

Crystallization (Comment)	Organism
at 4°C, using the hanging-drop vapor-diffusion method. SDH both in its ligand-free form and in complex with shikimate. Overall structure of apo-SDH is basically identical to that of the shikimate-SDH complex, both structures contain one molecule per asymmetric unit. Overall folding of SDH comprises the N-terminal alpha/beta domain for substrate binding and the C-terminal Rossmann fold for NADP binding. The active site is within a large groove between the two domains. Residue Tyr211 does not interact with shikimate in the binary SDH-shikimate complex structure. The main function of Tyr211 may be to stabilize the catalytic intermediate during catalysis. The NADP-binding domain of SDH is less conserved. The long helix specifically recognizing the adenine ribose phosphate is substituted with a short 310 helix in the NADP-binding domain. The interdomain angle of SDH is the widest among all known SDH structures, indicating an inactive open state of the SDH structure. Thus, a closing process may occur upon NADP+ binding to bring the cofactor close to the substrate for catalysis	Staphylococcus epidermidis RP62A

Crystallization (Comment)

Organism

at 4°C, using the hanging-drop vapor-diffusion method. SDH both in its ligand-free form and in complex with shikimate. Overall structure of apo-SDH is basically identical to that of the shikimate-SDH complex, both structures contain one molecule per asymmetric unit. Overall folding of SDH comprises the N-terminal alpha/beta domain for substrate binding and the C-terminal Rossmann fold for NADP binding. The active site is within a large groove between the two domains. Residue Tyr211 does not interact with shikimate in the binary SDH-shikimate complex structure. The main function of Tyr211 may be to stabilize the catalytic intermediate during catalysis. The NADP-binding domain of SDH is less conserved. The long helix specifically recognizing the adenine ribose phosphate is substituted with a short 310 helix in the NADP-binding domain. The interdomain angle of SDH is the widest among all known SDH structures, indicating an inactive open state of the SDH structure. Thus, a closing process may occur upon NADP+ binding to bring the cofactor close to the substrate for catalysis

Staphylococcus epidermidis RP62A

Protein Variants

Protein Variants	Comment	Organism
Y211F	results in a remarkable reduction in enzyme activity, leads to a significant decrease in kcat (345fold) and a minor increase in the Km (3fold) for shikimate. Tyr211 may play a major role in the catalytic process and a minor role in the initial substrate binding	Staphylococcus epidermidis RP62A

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.073	-	shikimate	wild-type	Staphylococcus epidermidis RP62A
0.1	-	NADP+	wild-type	Staphylococcus epidermidis RP62A
0.227	-	shikimate	mutant Y211F	Staphylococcus epidermidis RP62A
0.279	-	NADP+	mutant Y211F	Staphylococcus epidermidis RP62A
10.6	-	NAD+	wild-type	Staphylococcus epidermidis RP62A

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
31000	-	mutant Y211F, mass spectrometry	Staphylococcus epidermidis RP62A
31000	-	mutant Y211F, sequence analysis	Staphylococcus epidermidis RP62A
31010	-	recombinant SDH, mass spectrometry	Staphylococcus epidermidis RP62A
31010	-	recombinant SDH, sequence analysis	Staphylococcus epidermidis RP62A

Organism

Organism	UniProt	Comment	Textmining
Staphylococcus epidermidis RP62A	Q5HNV1	-	-

Purification (Commentary)

Purification (Comment)	Organism
one-step purification by nickel-affinity chromatography	Staphylococcus epidermidis RP62A

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
additional information	even in the presence of a high concentration of quinate (4 mM), SDH displays no activity using either NADP+ or NAD+ as a cofactor	Staphylococcus epidermidis RP62A	?	-	?
shikimate + NAD(P)+	-	Staphylococcus epidermidis RP62A	3-dehydroshikimate + NAD(P)H + H+	-	?
shikimate + NAD+	-	Staphylococcus epidermidis RP62A	3-dehydroshikimate + NADH + H+	-	r

Subunits

Subunits	Comment	Organism
monomer	gel filtration	Staphylococcus epidermidis RP62A

Synonyms

Synonyms	Comment	Organism
SDH	-	Staphylococcus epidermidis RP62A

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
0.066	-	shikimate	mutant Y211F	Staphylococcus epidermidis RP62A
22.8	-	shikimate	wild-type	Staphylococcus epidermidis RP62A
87	-	NAD+	wild-type	Staphylococcus epidermidis RP62A

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
11	-	-	Staphylococcus epidermidis RP62A

pH Range

pH Minimum	pH Maximum	Comment	Organism
7	12	-	Staphylococcus epidermidis RP62A

Cofactor

Cofactor	Comment	Organism	Structure
NAD(P)+	NADP+ is the preferred cofactor	Staphylococcus epidermidis RP62A