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Literature summary extracted from

  • Lee, D.; Kim, K.J.
    Structural insight into substrate specificity of 3-hydroxypropionyl-coenzyme A dehydratase from Metallosphaera sedula (2018), Sci. Rep., 8, 10692 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.2.1.116 gene Msed_2001, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic tree analysis, recombinant expression of C-terminally His6-tagged enzyme in Escherichia coli strain BL21 (DE3)-T1 Metallosphaera sedula

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.2.1.116 purified enzyme in complex with CoA, hanging drop vapor diffusion method, mixing of 0.001 ml of protein solution containing 41 mg/ml in 40 mM Tris-HCl, pH8.0, with 0.001 ml of reservoir solution, containing consisting of 10% w/v PEG 8000, 0.1 M sodium-potassium phosphate, pH 6.2, 0.2 M NaCl, and 10 mM EDTA, and equilibration against 0.05 ml of reservoir solution, 20°C, X-ray diffraction structure determination and analysis at 1.8 A resolution, modelling Metallosphaera sedula

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.2.1.116 3-hydroxypropanoyl-CoA Metallosphaera sedula
-
 acryloyl-CoA + H2O
-
 r
4.2.1.116 3-hydroxypropanoyl-CoA Metallosphaera sedula ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2
-
 acryloyl-CoA + H2O
-
 r

Organism

EC Number Organism UniProt Comment Textmining
4.2.1.116 Metallosphaera sedula A4YI89
-
-
4.2.1.116 Metallosphaera sedula ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 A4YI89
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.2.1.116 recombinant C-terminally His6-tagged enzyme from Escherichia coli strain BL21 (DE3)-T1 by nickel affinity chromatography and gel filtration to homogeneity Metallosphaera sedula

Reaction

EC Number Reaction Comment Organism Reaction ID
4.2.1.116 3-hydroxypropanoyl-CoA = acryloyl-CoA + H2O molecular mechanism, overview Metallosphaera sedula
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.2.1.116 3-hydroxypropanoyl-CoA
-
 Metallosphaera sedula acryloyl-CoA + H2O
-
 r
4.2.1.116 3-hydroxypropanoyl-CoA
-
 Metallosphaera sedula ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 acryloyl-CoA + H2O
-
 r
4.2.1.116 additional information substrate specificity of enzyme Ms3HPCD, modelling of 3-hydroxypropanoyl- and (S)-3-hydroxybutyryl-moiety binding mode of enzyme Ms3HPCD. The residues involved in the formation of the 3-hydroxypropanoate binding pocket are identified. Ms3HPCD cannot convert (R)-stereoisomer of 3-hydroxybutyryl-CoA. When (R)-3-hydroxybutyryl-CoA is used as a substrate, the positions of the 3-hydroxyl-group and the C4-moiety are reversed each other, resulting in improper positioning of the (R)-3-hydroxybutyryl-moiety in the pocket. Ms3HPCD has a tightly formed alpha3 helix near the active site, and bulky aromatic residues are located at the enoyl-group binding site, resulting in the enzyme having an optimal substrate binding site for accepting short-chain 3-hydroxyacyl-CoA as a substrate Metallosphaera sedula ?
-
 ?
4.2.1.116 additional information substrate specificity of enzyme Ms3HPCD, modelling of 3-hydroxypropanoyl- and (S)-3-hydroxybutyryl-moiety binding mode of enzyme Ms3HPCD. The residues involved in the formation of the 3-hydroxypropanoate binding pocket are identified. Ms3HPCD cannot convert (R)-stereoisomer of 3-hydroxybutyryl-CoA. When (R)-3-hydroxybutyryl-CoA is used as a substrate, the positions of the 3-hydroxyl-group and the C4-moiety are reversed each other, resulting in improper positioning of the (R)-3-hydroxybutyryl-moiety in the pocket. Ms3HPCD has a tightly formed alpha3 helix near the active site, and bulky aromatic residues are located at the enoyl-group binding site, resulting in the enzyme having an optimal substrate binding site for accepting short-chain 3-hydroxyacyl-CoA as a substrate Metallosphaera sedula ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 ?
-
 ?

Subunits

EC Number Subunits Comment Organism
4.2.1.116 ? x * 28300, about, sequence calculation Metallosphaera sedula

Synonyms

EC Number Synonyms Comment Organism
4.2.1.116 3-hydroxypropionyl-coenzyme A dehydratase
-
 Metallosphaera sedula
4.2.1.116 3HPCD
-
 Metallosphaera sedula
4.2.1.116 Ms3HPCD
-
 Metallosphaera sedula
4.2.1.116 Msed_2001
-
 Metallosphaera sedula

General Information

EC Number General Information Comment Organism
4.2.1.116 evolution Ms3HPCD shows an overall structure and the CoA-binding mode similar to other enoyl-CoA hydratase (ECH) family enzymes, but compared with the other ECHs, Ms3HPCD has a tightly formed alpha3 helix near the active site, and bulky aromatic residues are located at the enoyl-group binding site, resulting in the enzyme having an optimal substrate binding site for accepting short chain 3-hydroxyacyl-CoA as a substrate. Phylogenetic tree analysis. The 3HPCD homologues from the phylum Crenarchaeota have an enoyl-group binding pocket similar to that of bacterial short-chain ECHs Metallosphaera sedula
4.2.1.116 additional information molecular docking simulations of 3-hydroxypropanoyl-CoA and (S)-3-hydroxybutyryl-CoA to Ms3HPCD structure, overview. When (R)-3-hydroxybutyryl-CoA is used as a substrate, the positions of the 3-hydroxyl-group and the C4-moiety are reversed each other, resulting in improper positioning of the (R)-3-hydroxybutyryl-moiety in the pocket. Structural comparison of Ms3HPCD with other enoyl-CoA hydratases, Structural basis for 3-hydroxypropanoyl-CoA substrate specificity of Ms3HPCD and active site structure, overview. Glutamate residues, Glu113 and Glu133, which act as catalytic acid and base, respectively, are positioned at the active site of Ms3HPCD Metallosphaera sedula
4.2.1.116 physiological function Metallosphaera sedula is a thermoacidophilic autotrophic archaeon known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as carbon fixation pathway. 3-Hydroxypropionyl-CoA dehydratase (3HPCD) is an enzyme involved in the 3-HP/4-HB cycle by converting 3-hydroxypropionyl-CoA to acryloyl-CoA Metallosphaera sedula