Literature summary for 5.4.99.13 extracted from

Jost, M.; Born, D.A.; Cracan, V.; Banerjee, R.; Drennan, C.L.
Structural basis for substrate specificity in adenosylcobalamin-dependent isobutyryl-CoA mutase and related acyl-CoA mutases (2015), J. Biol. Chem., 290, 26882-26898 .

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Cloned(Commentary)

Cloned (Comment)	Organism
gene icmF, recombinant expression of N-terminally His-tagged IcmF	Cupriavidus metallidurans

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified enzyme in complex with four different substrates, GDP and isovaleryl-CoA, or isobutyryl-CoA or n-butytryl-CoA or pivalyl-CoA, hanging drop vapor diffusion technique, mixing of 0.001 ml of 11.7 mg/ml IcmF protein in 100 mM NaCl, 50 mM HEPES, pH 7.5, 1 mM GDP, 3 mM MgCl2, 0.3 mM AdoCbl, with 0.001 ml of reservoir solution containing 0.7-0.75 M potassium sodium tartrate, 0.2 M ammonium acetate, 0.1 M imidazole, pH 7.0-7.7, and 3% v/v ethylene glycol, and equilibration against 0.5 ml reservoir solution, 3-6 weeks, at 25°C, X-ray diffraction structure determination and analysis at 3.4-3.5 A resolution	Cupriavidus metallidurans

Crystallization (Comment)

Organism

purified enzyme in complex with four different substrates, GDP and isovaleryl-CoA, or isobutyryl-CoA or n-butytryl-CoA or pivalyl-CoA, hanging drop vapor diffusion technique, mixing of 0.001 ml of 11.7 mg/ml IcmF protein in 100 mM NaCl, 50 mM HEPES, pH 7.5, 1 mM GDP, 3 mM MgCl2, 0.3 mM AdoCbl, with 0.001 ml of reservoir solution containing 0.7-0.75 M potassium sodium tartrate, 0.2 M ammonium acetate, 0.1 M imidazole, pH 7.0-7.7, and 3% v/v ethylene glycol, and equilibration against 0.5 ml reservoir solution, 3-6 weeks, at 25°C, X-ray diffraction structure determination and analysis at 3.4-3.5 A resolution

Cupriavidus metallidurans

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Cupriavidus metallidurans

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
2-methylpropanoyl-CoA	Cupriavidus metallidurans	interconversion	butanoyl-CoA	-	r
2-methylpropanoyl-CoA	Cupriavidus metallidurans ATCC 43123	interconversion	butanoyl-CoA	-	r

Organism

Organism	UniProt	Comment	Textmining
Cupriavidus metallidurans	Q1LRY0	-	-
Cupriavidus metallidurans ATCC 43123	Q1LRY0	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant N-terminally His-tagged	Cupriavidus metallidurans

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
2-methylpropanoyl-CoA	interconversion	Cupriavidus metallidurans	butanoyl-CoA	-	r
2-methylpropanoyl-CoA	interconversion	Cupriavidus metallidurans ATCC 43123	butanoyl-CoA	-	r
isovaleryl-CoA	-	Cupriavidus metallidurans	pivalyl-CoA	-	r
isovaleryl-CoA	-	Cupriavidus metallidurans ATCC 43123	pivalyl-CoA	-	r
additional information	enzyme substrate specificity, active site architecture and determinants of substrate specificity, comparison of the substrate-bound structures to that of substrate-free holo-IcmF-GDP, overview. Acyl-CoA substrates are threaded through the TIM barrel substrate-binding domain	Cupriavidus metallidurans	?	-	?
additional information	enzyme substrate specificity, active site architecture and determinants of substrate specificity, comparison of the substrate-bound structures to that of substrate-free holo-IcmF-GDP, overview. Acyl-CoA substrates are threaded through the TIM barrel substrate-binding domain	Cupriavidus metallidurans ATCC 43123	?	-	?

Subunits

Subunits	Comment	Organism
dimer	-	Cupriavidus metallidurans

Synonyms

Synonyms	Comment	Organism
adenosylcobalamin-dependent isobutyryl-CoA mutase	-	Cupriavidus metallidurans
IcmF	-	Cupriavidus metallidurans
PCM	-	Cupriavidus metallidurans

Cofactor

Cofactor	Comment	Organism	Structure
5'-deoxyadenosylcobalamin	AdoCbl, required, two conformations: C3'-endo and C2'-endo, conformational change of the 5'-deoxyadenosyl group from C2'-endo to C3'-endo contributes to initiation of catalysis. Adenosylcobalamin (coenzyme B12) is an organometallic enzyme cofactor for radical chemistry. Its reactivity is based on a unique covalent cobalt-carbon (Co-C) bond that is sufficiently weak to allow for reversible homolytic cleavage in enzyme active sites, generating a 5'-deoxyadenosyl radical in the presence of an appropriate substrate. The radical can then abstract a substrate hydrogen atom and initiate difficult chemical transformations	Cupriavidus metallidurans

General Information

General Information	Comment	Organism
additional information	enzyme IcmF in general is a fusion between the radical B12 enzyme isobutyryl-CoA mutase and its G-protein chaperone. IcmF from Cupriavidus metallidurans, which also contains a G-protein domain in addition to the mutase domains, with AdoCbl in the ICM active site and GDP-Mg2+ in the G-protein active site (holo-IcmF-GDP)	Cupriavidus metallidurans