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Literature summary 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 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.2.7 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

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

Metals/Ions

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

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.1.2.7 17670
-
 cytochrome cL, gel filtration Methylophaga aminisulfidivorans

Natural Substrates/ Products (Substrates)

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

Organism

EC Number Organism UniProt Comment Textmining
1.1.2.7 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
-
1.1.2.7 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)

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

Subunits

EC Number Subunits Comment Organism
1.1.2.7 monomer 1 * 18000, cytochrome cL, SDS-PAGE Methylophaga aminisulfidivorans
1.1.2.7 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

EC Number Synonyms Comment Organism
1.1.2.7 MDH
-
 Methylophaga aminisulfidivorans
1.1.2.7 MxaJ
-
 Methylophaga aminisulfidivorans

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.2.7 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
1.1.2.7 heme c coordination in CtcL at the active site, structure, overview. Contains Fe2+ Methylophaga aminisulfidivorans
1.1.2.7 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
1.1.2.7 pyrroloquinoline quinone PQQ, active site bound Methylophaga aminisulfidivorans

General Information

EC Number General Information Comment Organism
1.1.2.7 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