Biosynthesis of Amino Acids, Nucleotides, and Related Molecules

Nitrogen fixation

the conversion of N2 to forms that can support life (NH3, NO2-, NO-)

Nitrification

the process of converting ammonia to nitric oxide, nitrite, and finally nitrate

Denitrification

reduction of nitrate and nitrite to N under anaerobic conditions

Anaerobic ammonia oxidation (anammox)

an alternative path back to atmospheric N2 that starts with ammonia and nitrite

• provided by a group of backteria

Nitrite assimilation

a two-step reductive process that bypasses atmospheric N2

Nitrate reductase

reduces NO3- to NO2-

• electrons flow from NADH through cysteine, FAD, a cytochrome (cyt b557) and a novel cofactor containing molybdenum, before reducing NO3-

Nitrite reductase

catalyzes a six-electron transfer that reduces NO2- to NH4+

Nitrogenase complex

highly conserved complex of proteins that carries out the fixation of N2 as NH3

• central components are dinitrogenase reductase and dinitrogenase

dinitrogenase reductase

a dimer of two identical subunits

dinitrogenase

an α₂β₂ tetramer with two Fe-containing cofactors that transfer electrons:

• P cluster

• FeMo cofactor

FeMo cofactor contains:

• 7 Fe atoms

• 9 S atoms

• 1 Mo atom

• 1 bound homocitrate

Electrons required for nitrogen fixation:

• 6 for the reduction of N₂

• 2 to produce one molecule of H₂

Glutamine synthetase

catalyzes the two-step rxn of NH₄+ with glutamate to produce glutamine

glutamate syntetase

catalyzes the formation of two molecules of glutamate from α-ketoglutarate and glutamine

Net rxn of glutamine synthetase and glutamate synthetase

α-ketoglutarate + NH_4⁺ + NAD(P)H + ATP —> glutamate + NAD(P)⁺ + ADP + P_i

Glutamate dehydrogenase

catalyzes the rxn of α-ketoglutarate and NH_4⁺ to form glutamate

3 classes of glutamine synthetases:

• GSI (found in bacteria): 12 identical subunits

• GSII (found in eukaryotes and some bacteria): 10 identical subunits

• GSIII (found in two bacterial species): double-ringed dodecamer of identical chains