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Literature summary extracted from

  • Son, H.F.; Kim, S.; Seo, H.; Hong, J.; Lee, D.; Jin, K.S.; Park, S.; Kim, K.J.
    Structural insight into bi-functional malonyl-CoA reductase (2020), Environ. Microbiol., 22, 752-765 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.2.1.75 expressed in Escherichia coli BL21(DE3) cells Erythrobacter dokdonensis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.1.298 crystallization trials of the full-length MCR fail, thus production of the N-terminal domain (MCRND, Met1-Pro567) and the C-terminal domain (MCRCD, Gly568-Val1230) separately, X-ray diffraction structure determination and analysis at resolutions of 2.20 and 1.80 A, respectively, by a single-wavelength anomalous dispersion (SAD) method Erythrobacter dokdonensis
1.2.1.75 crystallization trials of the full-length MCR fail, thus production of the N-terminal domain (MCRND, Met1-Pro567) and the C-terminal domain (MCRCD, Gly568-Val1230) separately, X-ray diffraction structure determination and analysis at resolutions of 2.20 and 1.80 A, respectively, by a single-wavelength anomalous dispersion (SAD) method Erythrobacter dokdonensis
1.2.1.75 N-terminal domain, hanging drop vapor diffusion method, using 10% (w/v) PEG3350, 200 mM lithium sulfate, 100 mM Tris-HCl, pH 8.0. C-terminal domain, hanging drop vapor diffusion method, using 1.6 M lithium sulfate and 100 mM HEPES, pH 8.0 Erythrobacter dokdonensis

Protein Variants

EC Number Protein Variants Comment Organism
1.2.1.75 I798A the mutant of the C-terminal domain shows less than 30% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 K195A the mutant of the N-terminal domain is almost completely inactive as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 K748A the mutant of the C-terminal domain is almost completely inactive as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 K802A the mutant of the C-terminal domain shows about 95% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 K926A the mutant of the C-terminal domain shows about 90% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 L790A inactive Erythrobacter dokdonensis
1.2.1.75 M662A the mutant of the C-terminal domain is almost completely inactive as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 N740A the mutant of the C-terminal domain shows about 15% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 N805A the mutant of the C-terminal domain shows less than 60% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 R1166A the mutant of the C-terminal domain shows less than 20% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 R188A the mutant of the N-terminal domain shows less than 10% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 R741A the mutant of the C-terminal domain shows less than 5% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 R780A the mutant of the C-terminal domain is almost completely inactive as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 R794A the mutant of the C-terminal domain is almost completely inactive as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 S726A the mutant of the C-terminal domain is almost completely inactive as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 T178A the mutant of the N-terminal domain is almost completely inactive as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 Y185A the mutant of the N-terminal domain shows less than 20% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 Y191A the mutant of the N-terminal domain shows less than 10% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 Y738A the mutant of the C-terminal domain shows about 10% activity as compared to the wild type enzyme Erythrobacter dokdonensis
1.2.1.75 Y744A the mutant of the C-terminal domain shows less than 5% activity as compared to the wild type enzyme Erythrobacter dokdonensis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.2.1.75 Mg2+ 1 mM used in assay conditions Erythrobacter dokdonensis

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.2.1.75 265000
-
 gel filtration Erythrobacter dokdonensis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.298 malonate semialdehyde + NADPH + H+ Erythrobacter dokdonensis
-
 3-hydroxypropanoate + NADP+
-
 ?
1.1.1.298 malonate semialdehyde + NADPH + H+ Erythrobacter dokdonensis DSW-74
-
 3-hydroxypropanoate + NADP+
-
 ?
1.2.1.75 malonate semialdehyde + NADPH + H+ Erythrobacter dokdonensis
-
 3-hydroxypropionic acid + NADP+
-
 ?
1.2.1.75 malonyl-CoA + NADPH + H+ Erythrobacter dokdonensis
-
 malonate semialdehyde + CoA + NADP+
-
 ?
1.2.1.75 malonyl-CoA + NADPH + H+ Erythrobacter dokdonensis DSW-74
-
 malonate semialdehyde + CoA + NADP+
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.298 Erythrobacter dokdonensis A0A1A7BFR5 Porphyrobacter dokdonensis
-
1.1.1.298 Erythrobacter dokdonensis DSW-74 A0A1A7BFR5 Porphyrobacter dokdonensis
-
1.2.1.75 Erythrobacter dokdonensis
-
-
-
1.2.1.75 Erythrobacter dokdonensis A0A1A7BFR5 Porphyrobacter dokdonensis
-
1.2.1.75 Erythrobacter dokdonensis DSW-74 A0A1A7BFR5 Porphyrobacter dokdonensis
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.2.1.75 Ni-NTA agarose column chromatography and Sephacryl S-300 gel filtration Erythrobacter dokdonensis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.298 malonate semialdehyde + NADPH + H+
-
 Erythrobacter dokdonensis 3-hydroxypropanoate + NADP+
-
 ?
1.1.1.298 malonate semialdehyde + NADPH + H+
-
 Erythrobacter dokdonensis DSW-74 3-hydroxypropanoate + NADP+
-
 ?
1.1.1.298 additional information the bifunctional malonyl-CoA reductase catalyzes the formation of malonate semialdehyde from malonyl-CoA, EC 1.2.1.75, and the reduction of malonate semialdehyde to 3-hydroxypropionate, molecular mechanism of the conversion of malonyl-CoA to 3-HP in the bacterial 3-HP pathway, substrate binding docking simulations, overview Erythrobacter dokdonensis ?
-
-
1.1.1.298 additional information the bifunctional malonyl-CoA reductase catalyzes the formation of malonate semialdehyde from malonyl-CoA, EC 1.2.1.75, and the reduction of malonate semialdehyde to 3-hydroxypropionate, molecular mechanism of the conversion of malonyl-CoA to 3-HP in the bacterial 3-HP pathway, substrate binding docking simulations, overview Erythrobacter dokdonensis DSW-74 ?
-
-
1.2.1.75 malonate semialdehyde + NADPH + H+
-
 Erythrobacter dokdonensis 3-hydroxypropionic acid + NADP+
-
 ?
1.2.1.75 malonyl-CoA + NADPH + H+
-
 Erythrobacter dokdonensis malonate semialdehyde + CoA + NADP+
-
 ?
1.2.1.75 malonyl-CoA + NADPH + H+
-
 Erythrobacter dokdonensis DSW-74 malonate semialdehyde + CoA + NADP+
-
 ?
1.2.1.75 additional information the bifunctional malonyl-CoA reductase catalyzes the formation of malonate semialdehyde from malonyl-CoA, and the reduction of malonate semialdehyde to 3-hydroxypropionate, cf. EC 1.1.1.298, molecular mechanism of the conversion of malonyl-CoA to 3-HP in the bacterial 3-HP pathway, substrate binding docking simulations, overview Erythrobacter dokdonensis ?
-
-
1.2.1.75 additional information the bifunctional malonyl-CoA reductase catalyzes the formation of malonate semialdehyde from malonyl-CoA, and the reduction of malonate semialdehyde to 3-hydroxypropionate, cf. EC 1.1.1.298, molecular mechanism of the conversion of malonyl-CoA to 3-HP in the bacterial 3-HP pathway, substrate binding docking simulations, overview Erythrobacter dokdonensis DSW-74 ?
-
-

Subunits

EC Number Subunits Comment Organism
1.1.1.298 homodimer subunit structures and interaction analysis Erythrobacter dokdonensis
1.1.1.298 More olecular architecture of the full-length MCR, modeling, overview Erythrobacter dokdonensis
1.2.1.75 homodimer x-ray crystallography Erythrobacter dokdonensis
1.2.1.75 homodimer subunit structures and interaction analysis Erythrobacter dokdonensis
1.2.1.75 More olecular architecture of the full-length MCR, modeling, overview Erythrobacter dokdonensis

Synonyms

EC Number Synonyms Comment Organism
1.1.1.298 bi-functional malonyl-CoA reductase
-
 Erythrobacter dokdonensis
1.1.1.298 malonate semialdehyde reductase
-
 Erythrobacter dokdonensis
1.1.1.298 MCR
-
 Erythrobacter dokdonensis
1.1.1.298 More see also EC 1.2.1.75 Erythrobacter dokdonensis
1.1.1.298 MSAR
-
 Erythrobacter dokdonensis
1.2.1.75 bi-functional malonyl-CoA reductase
-
 Erythrobacter dokdonensis
1.2.1.75 malonate semialdehyde reductase
-
 Erythrobacter dokdonensis
1.2.1.75 malonyl-CoA reductase
-
 Erythrobacter dokdonensis
1.2.1.75 MCR
-
 Erythrobacter dokdonensis
1.2.1.75 More see also EC 1.1.1.298 Erythrobacter dokdonensis
1.2.1.75 MSAR
-
 Erythrobacter dokdonensis

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.298 NADPH the NADPH cofactor bound in MCR N-terminal domain is stabilized by hydrogen bonds with the side chains of Arg55, Arg59, Asp84, Asn151, Tyr744 and Lys195, and the main chains of Asn34, Leu35, Gly85, Asn111, Gly113 and Ile224, and by interaction with C-terminal resdiues by hydrogen bonds with the side chains of Ser88, Arg611, Arg612, Asp646, Tyr744 and Lys748, and the main chains of Ser588, Ala589, Ile591, Arg611, Arg612, Val647, Asn673 and Val776, cofactor binding site structure, overview Erythrobacter dokdonensis
1.2.1.75 NADPH
-
 Erythrobacter dokdonensis
1.2.1.75 NADPH the NADPH cofactor bound in MCR N-terminal domain is stabilized by hydrogen bonds with the side chains of Arg55, Arg59, Asp84, Asn151, Tyr744 and Lys195, and the main chains of Asn34, Leu35, Gly85, Asn111, Gly113 and Ile224, and by interaction with C-terminal resdiues by hydrogen bonds with the side chains of Ser88, Arg611, Arg612, Asp646, Tyr744 and Lys748, and the main chains of Ser588, Ala589, Ile591, Arg611, Arg612, Val647, Asn673 and Val776, cofactor binding site structure, overview Erythrobacter dokdonensis

General Information

EC Number General Information Comment Organism
1.1.1.298 evolution distribution of bifunctional MCR in bacteria and comparison with archaeal MCR and MSAR, overview Erythrobacter dokdonensis
1.1.1.298 metabolism enzymes involved in archaeal and bacterial 3-HP pathway and their structures, overview Erythrobacter dokdonensis
1.1.1.298 additional information Tyr191 is the catalytic residue, active site structure, substrate binding mode, overview. Structure comparison with the archaeal MCR from Sulfurisphaera tokodaii (StMCR) Erythrobacter dokdonensis
1.2.1.75 evolution distribution of bifunctional MCR in bacteria and comparison with archaeal MCR and MSAR, overview Erythrobacter dokdonensis
1.2.1.75 metabolism enzymes involved in archaeal and bacterial 3-HP pathway and their structures, overview Erythrobacter dokdonensis
1.2.1.75 additional information Tyr191 is the catalytic residue, active site structure, substrate binding mode, overview. Structure comparison with the archaeal MCR from Sulfurisphaera tokodaii (StMCR) Erythrobacter dokdonensis