The process of coenzyme FO synthesis is facilitated by two separate free radical SAM active sites, one for each of the enzymes CofG, CofH, or FbiC. Fo synthase's functional domain is made up of these two SAM domains. Methanococcus jannaschii uses eight different enzymes to biosynthesize F420; the final step that needs to be figured out is how the deazoflavin chromophore (Fo) is formed [1]. A key low redox potential electron carrier in methanogenic metabolism is coenzyme F420. F420-dependent hydrogenase reduces coenzyme F420 in the presence of hydrogen gas [3]. The function of coenzyme F420 is to transfer hydrides to F420-specific glucose-6-phosphate dehydrogenase (Fgd) found in mycobacteria. Coenzyme F420 is involved in energy metabolism, NADP reduction, oxygen detoxification, and sulfite reduction. It is found in all methanogenic archaea and certain non-methanogenic archaea. Macrophages' antibacterial activities can be less effective against Mycobacterium tuberculosis when NO2 is converted back to NO using F420H2 [4].

Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the cytoplasmic protein and forms a huge complex consisting of FrhABG heterotrimers with each a [NiFe] center, four Fe-S clusters and an FAD. Here, we report the structure determined by near-atomic resolution cryo-EM of Frh with and without bound substrate F420. The polypeptide chains of FrhB, for which there was no homolog, was traced de novo from the EM map. The 1.2-MDa complex contains 12 copies of the heterotrimer, which unexpectedly form a spherical protein shell with a hollow core. The cryo-EM map reveals strong electron density of the chains of metal clusters running parallel to the protein shell, and the F420-binding site is located at the end of the chain near the outside of the spherical structure. DOI:http://dx.doi.org/10.7554/eLife.00218.001. [1]

---

Coenzyme F420 is a redox cofactor found in methanogens and in various actinobacteria. Despite the major biological importance of this cofactor, the biosynthesis of its deazaflavin core (8-hydroxy-5-deazaflavin, F(o)) is still poorly understood. F(o) synthase, the enzyme involved, is an unusual multidomain radical SAM enzyme that uses two separate 5'-deoxyadenosyl radicals to catalyze F(o) formation. In this paper, we report a detailed mechanistic study on this complex enzyme that led us to identify (1) the hydrogen atoms abstracted from the substrate by the two radical SAM domains, (2) the second tyrosine-derived product, (3) the reaction product of the CofH-catalyzed reaction, (4) the demonstration that this product is a substrate for CofG, and (5) a stereochemical study that is consistent with the formation of a p-hydroxybenzyl radical at the CofH active site. These results enable us to propose a mechanism for F(o) synthase and uncover a new catalytic motif in radical SAM enzymology involving the use of two 5'-deoxyadenosyl radicals to mediate the formation of a complex heterocycle. [2]

Coenzyme F420 is the central low-redox-potential electron carrier in methanogenic metabolism. The coenzyme is reduced under hydrogen by the action of F420-dependent hydrogenase. The standard free-energy change at pH 7 of F420 reduction was determined to be -15 kJ mol(-1), irrespective of the temperature (25-65 degrees C). Experiments performed with methane-forming cell suspensions of Methanothermobacter thermautotrophicus incubated under various conditions demonstrated that the ratios of reduced and oxidized F420 were in thermodynamic equilibrium with the gas-phase hydrogen partial pressures. During growth in a fed-batch fermenter, ratios changed in connection with the decrease in dissolved hydrogen. For most of the time, the changes were as expected for thermodynamic equilibrium between the oxidation state of F420 inside the cells and extracellular hydrogen. Also, methanol-metabolizing, but not acetate-converting, cells of Methanosarcina barkeri maintained the ratios of reduced and oxidized coenzyme F420 in thermodynamic equilibrium with external hydrogen. The results of the study demonstrate that F420 is a useful probe to assess in situ hydrogen concentrations in H2-metabolizing methanogens.[3]

---

In mycobacteria, F(420), a deazaflavin derivative, acts as a hydride transfer coenzyme for an F(420)-specific glucose-6-phosphate dehydrogenase (Fgd). Physiologically relevant reactions in the mycobacteria that use Fgd-generated reduced F(420) (F(420)H(2)) are unknown. In this work, F(420)H(2) was found to be oxidized by NO only in the presence of oxygen. Further analysis demonstrated that NO(2), produced from NO and O(2), was the oxidant. UV-visible spectroscopic and NO-sensor-based analyses proved that F(420)H(2) reduced NO(2) to NO. This reaction could serve as a defense system for Mycobacterium tuberculosis, which is more sensitive to NO(2) than NO under aerobic conditions. Activated macrophages produce NO, which in acidified phagosomes is converted to NO(2). Hence, by converting NO(2) back to NO with F(420)H(2), M. tuberculosis could decrease the effectiveness of antibacterial action of macrophages; such defense would correspond to active tuberculosis conditions where the bacterium grows aerobically. This hypothesis was consistent with the observation that a mutant strain of Mycobacterium smegmatis, a nonpathogenic relative of M. tuberculosis, which either did not produce or could not reduce F(420), was approximately 4-fold more sensitive to NO(2) than the wild-type strain. The phenomenon is reminiscent of the anticancer activity of gamma-tocopherol, which reduces NO(2) to NO and protects human cells from NO(2)-induced carcinogenesis. [2]

[1]. De novo modeling of the F(420)-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy. Elife. 2013;2:e00218. Published 2013 Mar 5.

[2]. Biosynthetic versatility and coordinated action of 5'-deoxyadenosyl radicals in deazaflavin biosynthesis. J Am Chem Soc. 2015;137(16):5406-5413.

[3]. Hydrogen concentrations in methane-forming cells probed by the ratios of reduced and oxidized coenzyme F420. Microbiology. 2005;151(Pt 5):1697‐1705.

[4]. Conversion of NO2 to NO by reduced coenzyme F420 protects mycobacteria from nitrosative damage. Proc Natl Acad Sci U S A. 2009;106(15):6333‐6338.

Factor Fo is a member of quinolines.
8-Hydroxy-5-deazaflavin has been reported in Methanothermobacter thermautotrophicus with data available.

C16H17N3O7

363.322084188461

363.107

37333-48-5

122079

Yellow to brown solid powder

-3

6

8

5

26

796

0

HJMIIBXYFPJZBP-UHFFFAOYSA-N

InChI=1S/C16H17N3O7/c20-6-12(23)13(24)11(22)5-19-10-4-8(21)2-1-7(10)3-9-14(19)17-16(26)18-15(9)25/h1-4,11-13,20,22-24H,5-6H2,(H2,17,18,25,26)

10-(2,3,4,5-tetrahydroxypentyl)-1H-pyrimido[4,5-b]quinoline-2,4,8-trione

8-Hydroxy-5-deazaflavin; Factor Fo; 10-(2,3,4,5-tetrahydroxypentyl)-1H-pyrimido[4,5-b]quinoline-2,4,8-trione; factor 420; 37333-48-5; 8-HDF cpd; F(420); DTXSID50958446;

2934.99.9001

Powder      -20°C    3 years

                     4°C     2 years

In solvent   -80°C    6 months

                  -20°C    1 month

Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)

DMSO : ~5 mg/mL (~13.76 mM)
Ethanol :< 1 mg/mL

Solubility in Formulation 1: 1 mg/mL (2.75 mM) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), suspension solution; with sonication.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 10.0 mg/mL clear DMSO stock solution to 400 μL of PEG300 and mix evenly; then add 50 μL of Tween-80 to the above solution and mix evenly; then add 450 μL of normal saline to adjust the volume to 1 mL.
Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution.

---

Solubility in Formulation 2: 0.53 mg/mL (1.46 mM) in 10% DMSO + 90% (20% SBE-β-CD in Saline) (add these co-solvents sequentially from left to right, and one by one), suspension solution; with ultrasonication.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 5.3 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly.
Preparation of 20% SBE-β-CD in Saline (4°C，1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution.

---

 (Please use freshly prepared in vivo formulations for optimal results.)