Protein Family Models

This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1]. [1]. 9036855. Crystal structure of formate dehydrogenase H: catalysis. involving Mo, molybdopterin, selenocysteine, and an Fe4S4. cluster.. Boyington JC, Gladyshev VN, Khangulov SV, Stadtman TC, Sun PD;. Science. 1997;275:1305-1308. (from Pfam)

Date:

2024-08-14

This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2]. [1]. 9818358. The formylmethanofuran dehydrogenase isoenzymes in. Methanobacterium wolfei and Methanobacterium. thermoautotrophicum: induction of the molybdenum isoenzyme by. molybdate and constitutive synthesis of the tungsten isoenzyme.. Hochheimer A, Hedderich R, Thauer RK;. Arch Microbiol 1998;170:389-393.. [2]. 8890912. Crystal structure of dimethyl sulfoxide reductase from. Rhodobacter capsulatus at 1.88 A resolution.. Schneider F, Lowe J, Huber R, Schindelin H, Kisker C, Knablein. J;. J Mol Biol 1996;263:53-69. (from Pfam)

Date:

2024-08-14

Date:

2024-08-14

This HMM describes a subset of formate dehydrogenase alpha chains found mainly in proteobacteria but also in Aquifex. The alpha chain contains domains for molybdopterin dinucleotide binding and molybdopterin oxidoreductase (PF01568 and PF00384, respectively). The holo-enzyme also contains beta and gamma subunits of 32 and 20 kDa. The enzyme catalyzes the oxidation of formate (produced from pyruvate during anaerobic growth) to carbon dioxide with the concomitant release of two electrons and two protons. The electrons are utilized mainly in the nitrate respiration by nitrate reductase [1]. In E. coli and Salmonella, there are two forms of the formate dehydrogenase, one induced by nitrate which is strictly anaerobic (fdn), and one incuced during the transition from aerobic to anaerobic growth (fdo). This subunit is one of only three proteins in E. coli which contain selenocysteine [2]. This model is well-defined, with a large, unpopulated trusted/noise gap.

Gene:

fdnG

Date:

2024-06-04