CO Dehydrogenase 3

Carbon monoxide dehydrogenase (CODH) is a bifunctional metalloenzyme that is found in acetogenic, methanogenic, and sulfate-reducing bacteria, and it fixes carbon on a global scale. It catalyzes the reversible conversion of CO to CO₂. Its bifunctional characteristic comes from coupling with acetal-CoA synthase (CODH/ACS), which is key in anaerobic carbon dioxide fixation.¹ Carbon monoxide dehydrogenase is a key component in several energy-yielding pathways in aerobic and anaerobic bacteria. There are two groups of carbon monoxide dehydrogenases, the Mo-Feflavin enzymes from aerobes and the Ni-Fe enzymes from anaerobes. Aerobic microbes use Mo-Fe-flavin CO dehydrogenase for oxidizing carbon monoxide in respiration.² Carbon monoxide dehydrogenase also initiates the conversion of CO to H₂ in phototrophic anaerobes which aids their growth.

Figure 1: Crystal structure of carbon monoxide dehydrogenase.³

Structure

Carbon monoxide dehydrogenase contains two metals, nickel and iron, and they are typically sites for where electrons tend to go towards. In carbon monoxide dehydrogenase, the metal that seems “central” and “available” is nickel, whereas the multiple iron atoms lack these attributes or are not as relatively “central” and “available” as nickel. From the infrared spectra of a nickel—CO complex, the first step in the oxidative mechanism of converting carbon monoxide to carbon dioxide is the binding of carbon monoxide to Ni²⁺ and the complexing of Fe²⁺ to a molecule of water.¹ An approaching carbon monoxide molecule would bond to the metal center—nickel—allowing the enzyme to perform its function. In the case of carbon monoxide dehydrogenase, the nickel has a charge of positive two, so it has six electrons in its 3d shell. Since carbon monoxide has a neutral charge, the charge on nickel will remain the same when CO attaches to it. Carbon monoxide dehydrogenase also has five amino acids in its structure, four of cysteine and one histidine. The cysteine amino acids are attached to sulfur atoms while histidine is to nitrogen. It also has four atoms of iron and one of nickel, where nickel is the active site.

When carbon dioxide bonds to nickel, the geometry of nickel shifts from a square planar to a square pyramidal⁴, as shown in Figure 2.⁵ The enzyme does not exhibit the exact geometries of a generic square plane or square pyramid, but these are the closest molecular shapes that they can relate to. According to the spectrochemical series, carbon monoxide is a strong field ligand, and from crystal field theory, strong field ligands exhibit large energy differences between non-degenerate orbitals. Therefore, electrons first fill up the lower energy orbitals before those of higher energy. Because of the approximate geometries of the enzyme, the shapes of a square plane and square pyramid must be assumed.

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Figure 2: Carbon monoxide dehydrogenase with (top) and without (bottom) the binding of CO.⁵

Symmetry

Nickel has six valence electrons in its 3d shell. From the crystal field splitting diagrams of the enzyme’s approximate geometries of a square plane and pyramid, the enzyme is equally diamagnetic whether the carbon monoxide molecule is attached to nickel or not, as shown in Figure 3 and Figure 4 respectively.

The molecular geometry of the nickel center is not perfectly square planar or square pyramidal. Furthermore, each ligand group of the four “corners” of the square are not identical; although the “corners” are made up of sulfur atoms, they are then bonded to different elements or compounds. Therefore, the only point group symmetry it exhibits is the identity (E), resulting in a symmetry of C1. The iron atoms have a similar case. None of the iron atoms in the enzyme have a symmetry element other than the identity (E) due to similar reasons in the case of nickel; they have no exact molecular geometry—only approximate—and have different ligand groups attached to them. Thus, the iron centers only have the identity (E) element, resulting in a symmetry of C1.

Figure 3: The crystal field splitting of the nickel Figure 4: The crystal field splitting of the nickel center with the binding of CO center without the binding of CO.

Function

Carbon monoxide dehydrogenase is also notable in various prokaryotic biochemical pathways, such as the metabolish of methanogenic, aerobic carboxidotrophic, acetogenic bacteria, sulfate-reducing, and hydrogenogenic bacteria.⁶ The reaction catalyzed by carbon monoxide dehydrogenase plays a significant role in the carbon cycle which allows organisms to use carbon monoxide as a source of energy and carbon.⁵ The reaction that CO dehydrogenase catalyzes is the oxidation of CO according to the following equation: CO + H₂O → CO₂ + 2 e⁻ + 2 H⁺.⁷ The enzyme is also significant in terms of monitoring environmental and atmospheric conditions in that microbial metabolisms of CO maintains ambient CO at safe levels to sustains other forms of life.⁸

Raman and Infrared Spectroscopy

Although Raman and IR spectra exists for carbon monoxide dehydrogenase, there are interactions and elements in the molecule—such as the carbon monoxide bond, the sulfur bonds, and the iron bonds—that could vibrate and appear on an infrared spectrum; but to determine the Raman spectroscopy, the exact character tables cannot be used due to the molecule’s lack of symmetry. Thus, determining which bands come from Raman and infrared spectroscopy cannot be done from the character tables alone. However, vibrations would occur, and most likely, the infrared spectrum would depict peaks of CO, S—Ni, S—Fe, and other stretches, bends, and twists of these bonds from vibrational modes.

References

1. Chen, J.; Huang, S.; Seravalli, J.; Gutzman Jr, H.; Swartz, D.J.; Ragsdale, S.W.; Bagley, K.A. (2003), "Infrared Studies of Carbon Monoxide Binding to Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase from Moorella thermoacetica", Biochemistry 42 (50): 14822–14830

2. Ferry J. G. (1995) "CO Dehydrogenase", Annu. Rev. Microbiol. 49:305-33

3. Carbon monoxide dehydrogenase: http://www.epidna.com/showabstract.php?pmid=11076018 (accessed May 23)

4. Dobbek, H.; Svetlitchnyi, V.; Gremer, L.; Huber, R.; Meyer, O. (2001), "Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S cluster"], Science 293 (5533): 1281

5. Carbon monoxide dehydrogenase: http://en.wikipedia.org/wiki/Carbon_..._dehydrogenase (accessed May 23).

6. Dobbek H, Svetlitchnyi V, Gremer L, Huber R, Meyer O (August 2001). "Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster". Science 293 (5533): 1281–5.

7. Meyer O., Gremer L., Ferner R., Ferner M., Dobbek H., Gnida M., Meyer-Klaucke W., Huber R. (2000), "The Role of Se, Mo and Fe in the Structure and Function of Carbon Monoxide Dehydrogenase", Biological Chemistry 381:865-876.

8. Bartholomew, G.W.; Alexander, M. (1979), "Microbial metabolism of carbon monoxide in culture and in soil", Applied and Environmental Microbiology 37 (5): 932, http://aem.asm.org/cgi/content/abstract/37/5/932