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Literature summary for 1.2.4.2 extracted from

  • Wagner, T.; Boyko, A.; Alzari, P.M.; Bunik, V.I.; Bellinzoni, M.
    Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate From a Michaelis-like complex to ThDP adducts (2019), J. Struct. Biol., 208, 182-190 .
    View publication on PubMed
Search for more literature for 1.2.4.2

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli Mycolicibacterium smegmatis

Crystallization (Commentary)

Crystallization (Comment) Organism
enzyme in complex with phosphono ethyl succinyl phosphonate and/or succinyl phosphonate, hanging drop vapor diffusion method, using 2% (w/v) 2-methyl-2-propanol and 47% (w/v) 2-methyl-2,4-pentanediol Mycolicibacterium smegmatis
in complex with inhibitors succinyl phosphonate, phosphono ethyl succinyl phosphonate. Crystallographic snapshots of the Michaelis-like complex, followed by the covalent adduction of the inhibitor to thiamin diphosphate, mimicking the pre-decarboxylation complex Mycolicibacterium smegmatis

Protein Variants

Protein Variants Comment Organism
E952Q in this mutant the activation of thiamine diphosphate is impaired Mycolicibacterium smegmatis

Inhibitors

Inhibitors Comment Organism Structure
phosphono ethyl succinyl phosphonate competitive inhibitor Mycolicibacterium smegmatis
succinyl phosphonate competitive inhibitor Mycolicibacterium smegmatis

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ 1 mM used in assay conditions Mycolicibacterium smegmatis

Organism

Organism UniProt Comment Textmining
Mycolicibacterium smegmatis A0R2B1
-
-
Mycolicibacterium smegmatis A0R2B1 cf. EC 4.1.1.71, EC 2.2.1.5 and EC 2.3.1.61
-
Mycolicibacterium smegmatis ATCC 700084 A0R2B1 cf. EC 4.1.1.71, EC 2.2.1.5 and EC 2.3.1.61
-
Mycolicibacterium smegmatis mc(2)155 A0R2B1
-
-

Purification (Commentary)

Purification (Comment) Organism
-
 Mycolicibacterium smegmatis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2-oxoglutarate + 2,6-dichlorophenolindophenol
-
 Mycolicibacterium smegmatis ?
-
 ?
2-oxoglutarate + 2,6-dichlorophenolindophenol
-
 Mycolicibacterium smegmatis ATCC 700084 ?
-
 ?
2-oxoglutarate + 2,6-dichlorophenolindophenol
-
 Mycolicibacterium smegmatis mc(2)155 ?
-
 ?

Synonyms

Synonyms Comment Organism
Kgd thiamine diphosphate-dependent E1o component of the 2-oxoglutarate dehydrogenase complex Mycolicibacterium smegmatis
SucA
-
 Mycolicibacterium smegmatis

Cofactor

Cofactor Comment Organism Structure
thiamine diphosphate
-
 Mycolicibacterium smegmatis
thiamine diphosphate dependent on Mycolicibacterium smegmatis

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.043
-
 succinyl phosphonate at pH 7.0 and 26°C Mycolicibacterium smegmatis
0.043
-
 succinyl phosphonate pH 7. 26°C Mycolicibacterium smegmatis
0.88
-
 phosphono ethyl succinyl phosphonate at pH 7.0 and 26°C Mycolicibacterium smegmatis
0.88
-
 phosphono ethyl succinyl phosphonate pH 7, 26°C Mycolicibacterium smegmatis