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Literature summary for 4.2.1.42 extracted from

  • Rakus, J.F.; Kalyanaraman, C.; Fedorov, A.A.; Fedorov, E.V.; Mills-Groninger, F.P.; Toro, R.; Bonanno, J.; Bain, K.; Sauder, J.M.; Burley, S.K.; Almo, S.C.; Jacobson, M.P.; Gerlt, J.A.
    Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis (2009), Biochemistry, 48, 11546-11558.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 4.2.1.42

Cloned(Commentary)

Cloned (Comment) Organism
into a TOPO vector (pSGX3), and transformed into Escherichia coli TOP10 competent cells. Gene in the pSGX3 vector transformed into Escherichia coli strains XL1-Blue for transformation and BL21(DE3) for expression Oceanobacillus iheyensis

Protein Variants

Protein Variants Comment Organism
H45Q has no detectable activity Oceanobacillus iheyensis
R162N retains a small amount of activity Oceanobacillus iheyensis
Y164F has no detectable activity Oceanobacillus iheyensis
Y90F is catalytically impaired. Structure of the mutant in complex with Mg2+ and galactarate has a well-defined C-terminal segment through residue 387, well-ordered electron density for galactarate, and Mg2+ ions in both metal sites for both protomers comprising the asymmetric unit Oceanobacillus iheyensis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.62
-
 galactarate wild-type, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis
2
-
 galactarate mutant Y90F, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis
4.4
-
 galactarate mutant H45Q, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ structure contains two Mg2+ ions located 10.4 A from one another, with one located in the canonical position in the (beta/alpha)7beta-barrel domain, the second is located in a site within the capping domain Oceanobacillus iheyensis

Organism

Organism UniProt Comment Textmining
Oceanobacillus iheyensis
-
-
-

Purification (Commentary)

Purification (Comment) Organism
by centrifugation, sonication, on Ni-NTA column and by gel filtration Oceanobacillus iheyensis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
galactarate
-
 Oceanobacillus iheyensis 5-dehydro-4-deoxy D-glucarate + H2O
-
 ?

Synonyms

Synonyms Comment Organism
galactarate dehydratase
-
 Oceanobacillus iheyensis
GalrD
-
 Oceanobacillus iheyensis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0013
-
 galactarate mutant H45Q, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis
0.0061
-
 galactarate mutant Y90F, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis
6.8
-
 galactarate wild-type, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.00029
-
 galactarate mutant H45Q, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis
0.00065
-
 galactarate mutant R162N, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis
0.0031
-
 galactarate mutant Y90F, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis
11
-
 galactarate wild-type, in 50 mM Hepes, pH 8.0, 5 mM MgCl2 Oceanobacillus iheyensis