Literature summary for 1.1.2.7 extracted from

Nojiri, M.; Hira, D.; Yamaguchi, K.; Okajima, T.; Tanizawa, K.; Suzuki, S.
Crystal structures of cytochrome c(L) and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and mechanistic insights into interactions between the two proteins (2006), Biochemistry, 45, 3481-3492.

Crystallization (Commentary)

Crystallization (Comment)	Organism
enzyme or cytochrome cL, hanging drop vapour diffusion method, 16°C, 0.001 ml of 20 mg/mL enzyme or cofactor in 40 mM Tris-HCl buffer, pH 7.5, is mixed with an equal volume of precipitant colution containing 0.2 M potassium thiocyanate and 20% PEG 3350 for the enzyme crystallization, and 2 mM ZnSO4, 20% PEG 10000, and 100 mM HEPES, pH 7.3, for the crystallization of Cyt cL, 1 week to 1 month, X-ray diffraction structure determination and analysis at 1.98-2.5 A resolution	Hyphomicrobium denitrificans
hanging-drop vapor diffusion method, X-ray structures of methanol dehydrogenase (Hd-MDH) and cytochrome cL at 2.5 A and 2.0 A resolution, respectively. Docking simulation between the coupled cytochrome cL molecules and the heterotetrameric methanol dehydrogenase	Hyphomicrobium denitrificans

Crystallization (Comment)

Organism

enzyme or cytochrome cL, hanging drop vapour diffusion method, 16°C, 0.001 ml of 20 mg/mL enzyme or cofactor in 40 mM Tris-HCl buffer, pH 7.5, is mixed with an equal volume of precipitant colution containing 0.2 M potassium thiocyanate and 20% PEG 3350 for the enzyme crystallization, and 2 mM ZnSO4, 20% PEG 10000, and 100 mM HEPES, pH 7.3, for the crystallization of Cyt cL, 1 week to 1 month, X-ray diffraction structure determination and analysis at 1.98-2.5 A resolution

Hyphomicrobium denitrificans

hanging-drop vapor diffusion method, X-ray structures of methanol dehydrogenase (Hd-MDH) and cytochrome cL at 2.5 A and 2.0 A resolution, respectively. Docking simulation between the coupled cytochrome cL molecules and the heterotetrameric methanol dehydrogenase

Hyphomicrobium denitrificans

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
additional information	-	additional information	steady-state and stopped-flow kinetics	Hyphomicrobium denitrificans
0.0003	-	ferricytochrome cL	pH 5.5, ionic strength: 0.0160 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.0006	-	ferricytochrome cL	pH 6.0, ionic strength: 0.0172 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.0011	-	ferricytochrome cL	pH 6.5, ionic strength: 0.0183 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.0026	-	ferricytochrome cL	pH 5.0, ionic strength: 0.0181 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.009	-	ferricytochrome cL	pH 4.5, ionic strength: 0.0168 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.105	-	ferricytochrome cL	pH 7.0, ionic strength: 0.0198 M, steady-state kinetic parameter	Hyphomicrobium denitrificans

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
9000	-	2 * 65000 + 2 * 9000	Hyphomicrobium denitrificans
65000	-	2 * 65000 + 2 * 9000	Hyphomicrobium denitrificans
148000	-	-	Hyphomicrobium denitrificans

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
methanol + 2 oxidized cytochrome cL	Hyphomicrobium denitrificans	way of electron transfer from methanol to O2, overview	formaldehyde + 2 reduced cytochrome cL	-	?
methanol + 2 oxidized cytochrome cL	Hyphomicrobium denitrificans A3151	way of electron transfer from methanol to O2, overview	formaldehyde + 2 reduced cytochrome cL	-	?
methanol + ferricytochrome cL	Hyphomicrobium denitrificans	-	formaldehyde + ferrocytochrome cL	-	?
methanol + ferricytochrome cL	Hyphomicrobium denitrificans A3151	-	formaldehyde + ferrocytochrome cL	-	?

Organism

Organism	UniProt	Comment	Textmining
Hyphomicrobium denitrificans	-	-	-
Hyphomicrobium denitrificans A3151	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
-	Hyphomicrobium denitrificans

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
additional information	-	-	Hyphomicrobium denitrificans
0.12	0.7	dependent on pH, overview	Hyphomicrobium denitrificans

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
methanol + 2 oxidized cytochrome cL	-	Hyphomicrobium denitrificans	formaldehyde + 2 reduced cytochrome cL	-	?
methanol + 2 oxidized cytochrome cL	way of electron transfer from methanol to O2, overview	Hyphomicrobium denitrificans	formaldehyde + 2 reduced cytochrome cL	-	?
methanol + 2 oxidized cytochrome cL	-	Hyphomicrobium denitrificans A3151	formaldehyde + 2 reduced cytochrome cL	-	?
methanol + 2 oxidized cytochrome cL	way of electron transfer from methanol to O2, overview	Hyphomicrobium denitrificans A3151	formaldehyde + 2 reduced cytochrome cL	-	?
methanol + ferricytochrome cL	-	Hyphomicrobium denitrificans	formaldehyde + ferrocytochrome cL	-	?
methanol + ferricytochrome cL	-	Hyphomicrobium denitrificans A3151	formaldehyde + ferrocytochrome cL	-	?

Subunits

Subunits	Comment	Organism
tetramer	alpha2beta2 structure, subunit organization and structure, docking model, overview	Hyphomicrobium denitrificans
tetramer	2 * 65000 + 2 * 9000	Hyphomicrobium denitrificans

Synonyms

Synonyms	Comment	Organism
Hd-MDH	-	Hyphomicrobium denitrificans
MDH	-	Hyphomicrobium denitrificans
methanol dehydrogenase	-	Hyphomicrobium denitrificans

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
25	-	assay at	Hyphomicrobium denitrificans

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
additional information	-	additional information	kcat at different pH, overview	Hyphomicrobium denitrificans
0.15	-	ferricytochrome cL	pH 5.5, ionic strength: 0.0160 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.21	-	ferricytochrome cL	pH 6.0, ionic strength: 0.0172 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.33	-	ferricytochrome cL	pH 6.5, ionic strength: 0.0183 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.41	-	ferricytochrome cL	pH 5.0, ionic strength: 0.0181 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.45	-	ferricytochrome cL	pH 4.5, ionic strength: 0.0168 M, steady-state kinetic parameter	Hyphomicrobium denitrificans
0.87	-	methanol	pH 7.0, 25°C	Hyphomicrobium denitrificans
0.87	-	ferricytochrome cL	pH 7.0, ionic strength: 0.0198 M, steady-state kinetic parameter	Hyphomicrobium denitrificans

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7	-	-	Hyphomicrobium denitrificans

pH Range

pH Minimum	pH Maximum	Comment	Organism
7	9	the enzyme oxidation step becomes rate-limiting at pH 9.0	Hyphomicrobium denitrificans

Cofactor

Cofactor	Comment	Organism	Structure
cytochrome cL	-	Hyphomicrobium denitrificans
pyrroloquinoline quinone	enzyme contains two semiquinone pyrroloquinoline quinone groups per heterotetramer	Hyphomicrobium denitrificans