Talk:Formate dehydrogenase

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Peer-review Hi, I really enjoyed your page! It is coming along really nicely! I think you should elaborate more on the transmembrane domain of formate dehydrogenase.Galanyousuf1 (talk) 04:26, 2 March 2015 (UTC)

Hey, I really enjoyed your page! It is coming along really nicely! I think you should elaborate more on the Reduction of Carbon dioxide/Oxidation of Formate by Molybdenum-Containing Formate Dehydrogenase. (talk)

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Molybdenum-Containing Formate Dehydrogenase
Molybdenum-Containing Formate Dehydrogenase in Sulfate-Reducing Bacteria Desulfovibrio desulfuricans (Dd FDH) :

The Sulfate-reducing bacteria of the Desulfovibrio genus contain diverse Mo-FDH enzymes which are able to catalyze the reversible two-electron oxidation of formate to carbon dioxide (equation 1). The Mo-FDH Enzymes contain one molybdenum atom coordinated by four sulfur atoms and the sulfo group and selenocysteine active sites. The molybdenum center is the active site, where formate is oxidized, while the other six redox centers are thought to be involved in the subsequent intramolecular electron transfer. The Sulfo active site Is the Direct Hydride Acceptor/Donor.

Equation (1): {\displaystyle {\ce {HCOO- <=> CO2 +2e- + H+}}}

Reduction of Carbon dioxide by Molybdenum-Containing Formate Dehydrogenase in Sulfate-Reducing Bacteria Desulfovibrio desulfuricans (Dd FDH) :

The first step in the reduction of Carbon dioxide by the enzyme Formate Dehydrogenase (FDH) found in the Sulfate-reducing bacteria of the Desulfovibrio genus is the transfer of hydride ion from the protonated sulfo group of the reduced molybdenum center (Mo4+-SH) to the carbon atom of carbon dioxide. After the hydride transfer, the molybdenum center is reduced from 6+ to 4+ by the intramolecular electron transfer of 2 electrons from the other redox centers, and the newly formed formate is released. The initial reduced active site center, Mo4+-SH, is regenerated by the protonation of the sulfo group coordinated to the reduced molybdenum center.

Oxidation of Formate by Molybdenum-Containing Formate Dehydrogenase in Sulfate-Reducing Bacteria Desulfovibrio desulfuricans (Dd FDH) :

The oxidation of the Formate is first initiated by formate binding to the oxidized active site, but not directly to the molybdenum atom. Thereafter, a hydride ion is transferred from formate to the sulfo group of the oxidized molybdenum center, Mo6+-S, leading to the formation of the reduced active site center, Mo4+-SH, and carbon dioxide. — Preceding unsigned comment added by Recyclingbin432 (talk • contribs) 03:54, 15 October 2019 (UTC)

Tweaking
The above draft is too awkward to be inserted. Please get your teacher to get off their ass and help you. Be attentive to capitalization.--Smokefoot (talk) 10:31, 15 October 2019 (UTC) Molybdenum-Containing formate dehydrogenase in the sulfate-reducing bacterium Desulfovibrio desulfuricans (Dd FDH) :

The sulfate-reducing bacteria of the genus Desulfovibrio contain diverse Mo-FDH enzymes, which are able to catalyze the reversible two-electron oxidation of formate to carbon dioxide (equation 1). The Mo-FDH enzymes contain one molybdenum atom coordinated by four sulfur atoms THE FOLLOWING IS GIBBERISHand the sulfo group and selenocysteine active sites. THE FOLLOWING IS VERY AWKWARD ENGLISH The molybdenum center is the active site, where formate is oxidized, while the other six redox centers are thought to be involved in the subsequent intramolecular electron transfer. THE FOLLOWING ENGLISH IS TOO AWKWARD: The Sulfo active site Is the Direct Hydride Acceptor/Donor. WHAT IS A SULFO GROUP?

Draft content submitted by wikiedu.org student Recyclingbin432 @ 13:39, 3 December 2019
Molybdenum-Containing Formate Dehydrogenase in Sulfate-Reducing Bacteria Desulfovibrio desulfuricans (Dd FDH) – new content for new subtopic:

The Sulfate-reducing bacteria of the Desulfovibrio genus contain diverse Mo-FDH enzymes which are able to catalyze the reversible two-electron oxidation of formate to carbon dioxide (equation 1). The Mo-FDH Enzymes contain one molybdenum atom coordinated by four sulfur atoms and a sulfo group and a selenocysteine group.

There are two active sites that play key roles in the conversion of formate to carbon dioxide. The first active site occurs at the molybdenum center, where the formate is oxidized while the second active site is at the sulfo ligand, where the installation and removal of hydride occurs.

Equation (1):

Reduction of Carbon dioxide by Molybdenum-Containing Formate Dehydrogenase in Sulfate-Reducing Bacteria Desulfovibrio desulfuricans (Dd FDH) – new content for new subtopic:

For FDH, the first step in the reduction of carbon dioxide is the removal of hydride ion from the previously protonated sulfo group and the addition of the removed ion to the carbon atom in carbon dioxide. After the hydride transfer, the molybdenum center is reduced from 6+ to 4+ by the intramolecular electron transfer of 2 electrons, and release of the newly formed formate. The active site, Mo4+-SH, which had been reduced previously is regenerated by the protonation of the sulfo group.

Oxidation of Formate by Molybdenum-Containing Formate Dehydrogenase in Sulfate-Reducing Bacteria Desulfovibrio desulfuricans (Dd FDH) new content for new subtopic:

In order for formate to be oxidized, the substrate needs to bind to the active site, that had been previously oxidized, but not straight to the metal center. Thereafter, a hydride ion is transferred to the oxidized molybdenum center, Mo6+-S, leading to the formation of the reduced active site center, Mo4+-SH, and carbon dioxide.

New Content for New Subtopic: Use of Formate Dehydrogenase in Photoreduction Nanoporous Reactors

Formate Dehydrogenase has been used in reactor devices, along with Ru(bpy)32+ (photosensitizer) and MV•+ (reduced Methyl Viologen, an electron mediator) in nanopores inside PGP50 (porous glass plate with nanopore diameter of 50 nm) in order to reduce carbon dioxide to formic acid under ambient conditions. The production of formic acid in the reactor device was shown to be greater in comparison to solution containing the same redox components in a homogeneous solution alone where the production of formic acid in the reactor device was shown to be 14 times higher than that in a solution alone.

In addition, the electron transfer efficiency from MV•+ to FDH in the reactor device was increased by twenty-two percent when compared to the solution, which was determined to be the rate limiting step. In addition, the use as an artificial coenzyme in the reactor device had a significant effect on the production of formic acid when compared to the naturally occurring enzyme. When the reduced form of methyl viologen (MV•+) was used as an artificial coenzyme, the production of formic acid is twenty times higher in comparison to the naturally occurring enzyme nicotinamide adenine dinucleotide (NADH) because the reverse reaction of formic acid to carbon dioxide was repressed.

New Content for New Subtopic: Sulfur shift in Mo-Containing Formate Dehydrogenase

The sulfur shift mechanism observed in Mo-Containing Formate Dehydrogenase allows the enzyme to alternate between two different states which can either permit or not permit for the binding of a substrate to the metal center (molybdenum), all while keeping the metal center hexa-coordinated to six ligands and the oxidation state remaining the same (+4). The state of Formate Dehydrogenase that does not permit the binding substrate (formate ) is a direct result of the quasi-covalent bond that is formed between the sulfur ligand and the fifth ligand (SeCys); while the fifth ligand is in the first coordination shell. While the state of Formate Dehydrogenase that permits for the binding of the substrate occurs by the opening a new coordination shell for the substrate to bind to the metal center. The opening and subsequent binding of the substrate first occurs by the substrate (formate) coming into close proximity to the metal center which causes the fifth ligand (SeCys) to move from the first coordination shell into the second coordination shell while at the same time sulfur ligand moves into the coordination shell that was previously occupied by the fifth ligand before the substrate came into proximity with the metal center. As the substrate moves closer to the metal center, the fifth ligand moves further away from the metal and eventually the substrate binds directly to the metal center.

Comment on the above: Please do not cite Wikipedia as a source for Wikipedia articles. This is WP:CIRCULAR referencing. Cite reliable independent sources. wbm1058 (talk) 16:24, 14 December 2019 (UTC)

Wiki Education assignment: CHEM 4610 F22
— Assignment last updated by Swiftie1999 (talk) 03:37, 25 September 2022 (UTC)

new content for Formate Dehydrogenase catalyzed formate oxidation and carbon dioxide reduction
Formate oxidation (Figure 1A) is initiated by the formate ion strongly binding to the Arg446 side chain and weakly forming Hydrogen bonds with the backbone of His448. This allows the ion to position itself so that the C-H bond is close to the sulfide ligand of the FDH catalytic active site. The molybdenum metal ion has an oxidation state of 6+ in this first step. The active site positions the side chain of arginine and asparagine residue to facilitate driving the C α hydrogen of formate toward the sulfide ligand. There is a hydride transfer over to the sulfido ligand with a consequent transfer of two electrons from the sulfido ligand to the Mo 6+ producing Mo+4 and -SH ligand (Figure 1A). In the last step, the molybdenum center is oxidized to +6 by an electron transfer. The oxidation decreases the pKa of the sulfide ligand which leads to deprotonation and the sulphur atoms forms a double bond with the molybdenum center and the initial FDH catalytic site with 6+ oxidation state is regenerated.

Carbon dioxide reduction is the reverse mechanism of formate oxidation (Figure 1B). In this process, the conserved arginine binds carbon dioxide to the reduced Mo4+ in the active site. In the next step, there is a hydride transfer from the sulfide ligand (Mo4+-SH) to the carbon of the carbon dioxide producing a formate moiety, the molybdenum center gains an oxidation state of 6+ in the process. In the last step of the catalytic cycle, the molybdenum center is reduced from Mo+6 to Mo+4 through intramolecular electron transfer as shown in the last step of reaction mechanism(figure 1B). After the release of the formate ion, the initial Mo6+ is regenerated.

This section describes the step by step reaction mechanism for formate dehydrogenase catalyzed oxidation and reduction. It includes figures of the mechanism and close up of the molybdenum active site of formate dehydrogenase from E. coli. Swiftie1999 (talk) 02:31, 6 December 2022 (UTC)