Effect of Metal Ions on the Activity of Ten NAD-Dependent Formate Dehydrogenases

Bulut H., Valjakka J., Yuksel B., Yilmazer B., Turunen O., BİNAY B.

PROTEIN JOURNAL, vol.39, no.5, pp.519-530, 2020 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 39 Issue: 5
  • Publication Date: 2020
  • Doi Number: 10.1007/s10930-020-09924-x
  • Journal Name: PROTEIN JOURNAL
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Agricultural & Environmental Science Database, Aquatic Science & Fisheries Abstracts (ASFA), BIOSIS, CAB Abstracts, Chemical Abstracts Core, EMBASE, MEDLINE, Veterinary Science Database
  • Page Numbers: pp.519-530
  • Istanbul Technical University Affiliated: Yes


NAD-dependent formate dehydrogenase (FDH) enzymes are frequently used in industrial and scientific applications. FDH is a reversible enzyme that reduces the NAD molecule to NADH and produces CO(2)by oxidation of the formate ion, whereas it causes CO(2)reduction in the reverse reaction. Some transition metal elements - Fe3+, Mo(6+)and W6 +- can be found in the FDH structure of anaerobic and archaeal microorganisms, and these enzymes require cations and other redox-active cofactors for their FDH activity. While NAD-dependent FDHs do not necessarily require any metal cations, the presence of various metal cations can still affect FDH activities. To study the effect of 11 different metal ions, NAD-dependent FDH enzymes from ten different microorganisms were tested:Ancylobacter aquaticus(AaFDH),Candida boidinii(CboFDH),Candida methylica(CmFDH),Ceriporiopsis subvermispora(CsFDH),Chaetomium thermophilum(CtFDH),Moraxellasp. (MsFDH),Myceliophthora thermophila(MtFDH),Paracoccussp. (PsFDH),Saccharomyces cerevisiae(ScFDH) andThiobacillussp. (TsFDH). It was found that metal ions (mainly Cu(2+)and Zn2+) could have quite strong inhibition effects on several enzymes in the forward reaction, whereas several cations (Li+, Mg2+, Mn2+, Fe(3+)and W6+) could increase the forward reaction of two FDHs. The highest activity increase (1.97 fold) was caused by Fe(3+)in AaFDH. The effect on the reverse reaction was minimal. The modelled structures of ten FDHs showed that the active site is formed by 15 highly conserved amino acid residues spatially settling around the formate binding site in a conserved way. However, the residue differences at some of the sites close to the substrate do not explain the activity differences. The active site space is very tight, excluding water molecules, as observed in earlier studies. Structural examination indicated that smaller metal ions might be spaced close to the active site to affect the reaction. Metal ion size showed partial correlation to the effect on inhibition or activation. Affinity of the substrate may also affect the sensitivity to the metal's effect. In addition, amino acid differences on the protein surface may also be important for the metal ion effect.