Literature summary for 1.1.2.7 extracted from

Ghosh, S.; Dhanasingh, I.; Ryu, J.; Kim, S.W.; Lee, S.H.
Crystal structure of cytochrome cL from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP (2020), J. Microbiol. Biotechnol., 30, 1261-1271 .

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified heme c containing CytcL from Methylophaga aminisulfidivorans (Ma-CytcL), hanging drop vapor diffusion method, mixing of 0.001 ml of 12 mg/ml protein solution containing 800 mM sodium phosphate monobasic, 100 mM HEPES/sodium hydroxide, pH 7.5, with 0.001 ml of reservoir solution containing 0.2 M lithium sulfate monohydrate, 0.1 M bis-Tris, pH 5.5, and 25% PEG 3350, at 20°C for 21 days, X-ray diffraction structure determination analysis at 2.13 A resolution, molecular replacement using the structures of cytochrome cL from Methylobacterium extorquens (Me-CytcL, PDB ID 2C8S) and Hyphomicrobium denitrificans (Hd-CytcL, PDB ID 2D0W) as model structures, modeling	Methylophaga aminisulfidivorans

Crystallization (Comment)

Organism

purified heme c containing CytcL from Methylophaga aminisulfidivorans (Ma-CytcL), hanging drop vapor diffusion method, mixing of 0.001 ml of 12 mg/ml protein solution containing 800 mM sodium phosphate monobasic, 100 mM HEPES/sodium hydroxide, pH 7.5, with 0.001 ml of reservoir solution containing 0.2 M lithium sulfate monohydrate, 0.1 M bis-Tris, pH 5.5, and 25% PEG 3350, at 20°C for 21 days, X-ray diffraction structure determination analysis at 2.13 A resolution, molecular replacement using the structures of cytochrome cL from Methylobacterium extorquens (Me-CytcL, PDB ID 2C8S) and Hyphomicrobium denitrificans (Hd-CytcL, PDB ID 2D0W) as model structures, modeling

Methylophaga aminisulfidivorans

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
extracellular	solute-binding protein MxaJ	Methylophaga aminisulfidivorans	-	-
periplasm	-	Methylophaga aminisulfidivorans	-	-

Metals/Ions

Metals/Ions	Comment	Organism
Ca2+	binds to cofactor CytcL, binding site analysis	Methylophaga aminisulfidivorans
Fe2+	in heme c, which is contained in cofactor cytochrome cL, and bound to CytcL, binding sites analysis	Methylophaga aminisulfidivorans
Na+	binds to cofactor CytcL, binding site analysis	Methylophaga aminisulfidivorans

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
17670	-	cytochrome cL, gel filtration	Methylophaga aminisulfidivorans

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
methanol + 2 cytochrome cL	Methylophaga aminisulfidivorans	-	formaldehyde + 2 reduced cytochrome cL	-	?
methanol + 2 cytochrome cL	Methylophaga aminisulfidivorans MP	-	formaldehyde + 2 reduced cytochrome cL	-	?

Organism

Organism	UniProt	Comment	Textmining
Methylophaga aminisulfidivorans	A3FJ48 AND A3FJ51 AND A3FJ49	subunits alpha and beta, and extracellular solute-binding protein MxaJ; an aquatic methylotrophic bacterium isolated from the sea waters of Mokpo, South Korea, a neutrophilic, moderately halophilic, and vitamin B12-independent facultative methylotroph	-
Methylophaga aminisulfidivorans MP	A3FJ48 AND A3FJ51 AND A3FJ49	subunits alpha and beta, and extracellular solute-binding protein MxaJ; an aquatic methylotrophic bacterium isolated from the sea waters of Mokpo, South Korea, a neutrophilic, moderately halophilic, and vitamin B12-independent facultative methylotroph	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
methanol + 2 cytochrome cL	-	Methylophaga aminisulfidivorans	formaldehyde + 2 reduced cytochrome cL	-	?
methanol + 2 cytochrome cL	-	Methylophaga aminisulfidivorans MP	formaldehyde + 2 reduced cytochrome cL	-	?

Subunits

Subunits	Comment	Organism
monomer	1 * 18000, cytochrome cL, SDS-PAGE	Methylophaga aminisulfidivorans
More	the overall interaction between beta-subunits and alpha-subunits of Ma-MDH is stronger than that of terrestrial homologues, providing the structural integrity to Ma-MDH in aquatic environments	Methylophaga aminisulfidivorans

Synonyms

Synonyms	Comment	Organism
MDH	-	Methylophaga aminisulfidivorans
MxaJ	-	Methylophaga aminisulfidivorans

Cofactor

Cofactor	Comment	Organism
cytochrome cL	Ma-CytcL, contains heme c and has unique features compared to those of the terrestrial homologues. Apart from Fe2+ in heme, three additional metal ion binding sites for Na+, Ca2+, and Fe2+ are found, wherein the ions mostly form coordination bonds with the amino acid residues on the loop (G93-Y111) that interacts with heme. These ions seem to enhance the stability of heme insertion by increasing the loop's steadiness. The basic N-terminal end, together with helix alpha4 and loop G126-Y136, contributes positive charge to the region. In contrast, the acidic C-terminal end provides a negatively charged surface, yielding several electrostatic contact points with partner proteins for electron transfer. The need for an adapter protein bridging MDH to CytcL within appropriate proximity for electron transfer is satisfied by protein MxaJ. Native Ma-CytcL is purified from Methylophaga aminisulfidivorans cell culture by anion exchange chromatography and gel filtration. It contains a signal peptide, sequence comparisons and metal binding sites analysis, overview	Methylophaga aminisulfidivorans
heme c	coordination in CtcL at the active site, structure, overview. Contains Fe2+	Methylophaga aminisulfidivorans
additional information	Ma-MxaJ contains the bi-lobate folding architecture found in periplasmic binding proteins (PDB ID 5SV6), presence of an acidic cavity at the interface of the two domains	Methylophaga aminisulfidivorans
pyrroloquinoline quinone	PQQ, active site bound	Methylophaga aminisulfidivorans

General Information

General Information	Comment	Organism
physiological function	cytochrome cL (CytcL) is an essential protein in the process of methanol oxidation in methylotrophs. It receives an electron from the pyrroloquinoline quinone (PQQ) cofactor of methanol dehydrogenase (MDH) to produce formaldehyde, direct electron transfer mechanism between CytcL and MDH, mechanism, overview. The need for an adapter protein bridging MDH to CytcL within appropriate proximity for electron transfer is satisfied by protein MxaJ	Methylophaga aminisulfidivorans