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Literature summary 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.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.25 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)

EC Number Crystallization (Comment) Organism
1.1.1.25 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

EC Number Protein Variants Comment Organism
1.1.1.25 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]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.25 0.073
-
 shikimate wild-type Staphylococcus epidermidis RP62A
1.1.1.25 0.1
-
 NADP+ wild-type Staphylococcus epidermidis RP62A
1.1.1.25 0.227
-
 shikimate mutant Y211F Staphylococcus epidermidis RP62A
1.1.1.25 0.279
-
 NADP+ mutant Y211F Staphylococcus epidermidis RP62A
1.1.1.25 10.6
-
 NAD+ wild-type Staphylococcus epidermidis RP62A

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.1.1.25 31000
-
 mutant Y211F, mass spectrometry Staphylococcus epidermidis RP62A
1.1.1.25 31000
-
 mutant Y211F, sequence analysis Staphylococcus epidermidis RP62A
1.1.1.25 31010
-
 recombinant SDH, mass spectrometry Staphylococcus epidermidis RP62A
1.1.1.25 31010
-
 recombinant SDH, sequence analysis Staphylococcus epidermidis RP62A

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.25 Staphylococcus epidermidis RP62A Q5HNV1
-
-

Purification (Commentary)

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

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.25 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 ?
-
 ?
1.1.1.25 shikimate + NAD(P)+
-
 Staphylococcus epidermidis RP62A 3-dehydroshikimate + NAD(P)H + H+
-
 ?
1.1.1.25 shikimate + NAD+
-
 Staphylococcus epidermidis RP62A 3-dehydroshikimate + NADH + H+
-
 r

Subunits

EC Number Subunits Comment Organism
1.1.1.25 monomer gel filtration Staphylococcus epidermidis RP62A

Synonyms

EC Number Synonyms Comment Organism
1.1.1.25 SDH
-
 Staphylococcus epidermidis RP62A

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.25 0.066
-
 shikimate mutant Y211F Staphylococcus epidermidis RP62A
1.1.1.25 22.8
-
 shikimate wild-type Staphylococcus epidermidis RP62A
1.1.1.25 87
-
 NAD+ wild-type Staphylococcus epidermidis RP62A

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.1.1.25 11
-
-
 Staphylococcus epidermidis RP62A

pH Range

EC Number pH Minimum pH Maximum Comment Organism
1.1.1.25 7 12
-
 Staphylococcus epidermidis RP62A

Cofactor

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