6VX0

Crystal structure of air-exposed C45G/T50C D. vulgaris carbon monoxide dehydrogenase (2 hour air exposure)

Summary for 6VX0

• Entry DOI: 10.2210/pdb6vx0/pdb
• Descriptor: Carbon monoxide dehydrogenase, IRON/SULFUR CLUSTER, Fe(4)-Ni(1)-S(4) cluster, oxidized, ... (5 entities in total)
• Functional Keywords: nickel-iron-sulfur (ni-fe-s) cluster, iron-sulfur (fe-s) cluster, metalloenzyme, oxidoreductase
• Biological source: Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
• Total number of polymer chains: 2
• Total formula weight: 135029.46

Authors

Wittenborn, E.C.,Drennan, C.L. (deposition date: 2020-02-20, release date: 2020-07-29, Last modification date: 2023-10-11)

Primary citation

Wittenborn, E.C.,Guendon, C.,Merrouch, M.,Benvenuti, M.,Fourmond, V.,Leger, C.,Drennan, C.L.,Dementin, S.
The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance inDesulfovibrio vulgarisNi-Fe Carbon Monoxide Dehydrogenase.
Acs Catalysis, 10:7328-7335, 2020

PubMed Abstract: Ni-Fe CO-dehydrogenases (CODHs) catalyze the conversion between CO and CO using a chain of Fe-S clusters to mediate long-range electron transfer. One of these clusters, the D-cluster, is surface-exposed and serves to transfer electrons between CODH and external redox partners. These enzymes tend to be extremely O-sensitive and are always manipulated under strictly anaerobic conditions. However, the CODH from (Dv) appears unique: exposure to micromolar concentrations of O on the minutes-time scale only reversibly inhibits the enzyme, and full activity is recovered after reduction. Here, we examine whether this unusual property of Dv CODH results from the nature of its D-cluster, which is a [2Fe-2S] cluster, instead of the [4Fe-4S] cluster observed in all other characterized CODHs. To this aim, we produced and characterized a Dv CODH variant where the [2Fe-2S] D-cluster is replaced with a [4Fe-4S] D-cluster through mutagenesis of the D-cluster-binding sequence motif. We determined the crystal structure of this CODH variant to 1.83-Å resolution and confirmed the incorporation of a [4Fe-4S] D-cluster. We show that upon long-term O-exposure, the [4Fe-4S] D-cluster degrades, whereas the [2Fe-2S] D-cluster remains intact. Crystal structures of the Dv CODH variant exposed to O for increasing periods of time provide snapshots of [4Fe-4S] D-cluster degradation. We further show that the WT enzyme purified under conditions retains 30% activity relative to a fully purification, compared to 10% for the variant, and the WT enzyme loses activity more slowly than the variant upon prolonged aerobic storage. The D-cluster is therefore a key site of irreversible oxidative damage in Dv CODH, and the presence of a [2Fe-2S] D-cluster contributes to the O-tolerance of this enzyme. Together, these results relate O-sensitivity with the details of the protein structure in this family of enzymes.

PubMed: 32655979
DOI: 10.1021/acscatal.0c00934

Experimental method

X-RAY DIFFRACTION (2.21 Å)