Identification and characterization of functional homologs of nitrogenase cofactor biosynthesis protein NifB from methanogens

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 112; no. 48; pp. 14829 - 14833
• Main Authors: Fay, Aaron W., Wiig, Jared A., Lee, Chi Chung, Hu, Yilin
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 01.12.2015; National Acad Sciences
• Subjects: Archaeal Proteins - chemistry; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Azotobacter vinelandii - enzymology; Azotobacter vinelandii - genetics; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding sites; Biological Sciences; Biosynthesis; Catalysis; Iron Compounds - chemistry; Iron Compounds - metabolism; Methanobacterium - enzymology; Methanobacterium - genetics; Methanosarcina - enzymology; Methanosarcina - genetics; Microorganisms; Protein Structure, Tertiary; Proteins; S-Adenosylmethionine - chemistry; S-Adenosylmethionine - metabolism; NifB; radical SAM; homologs; methanogens; nitrogenase
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1510409112

Nitrogenase biosynthesis protein NifB catalyzes the radicalS-adenosyl-L-methionine (SAM)-dependent insertion of carbide into the M cluster, the cofactor of the molybdenum nitrogenase fromAzotobacter vinelandii.Here, we report the identification and characterization of two naturally “truncated” homologs of NifB fromMethanosarcina acetivorans(NifB Ma ) andMethanobacterium thermoautotrophicum(NifB Mt ), which contain a SAM-binding domain at the N terminus but lack a domain toward the C terminus that shares homology with NifX, an accessory protein in M cluster biosynthesis. NifB Ma and NifB Mt are monomeric proteins containing a SAM-binding [Fe₄S₄] cluster (designated the SAM cluster) and a [Fe₄S₄]-like cluster pair (designated the K cluster) that can be processed into an [Fe₈S₉] precursor to the M cluster (designated the L cluster). Further, the K clusters in NifB Ma and NifB Mt can be converted to L clusters upon addition of SAM, which corresponds to their ability to heterologously donate L clusters to the biosynthetic machinery ofA. vinelandiifor further maturation into the M clusters. Perhaps even more excitingly, NifB Ma and NifB Mt can catalyze the removal of methyl group from SAM and the abstraction of hydrogen from this methyl group by 5′-deoxyadenosyl radical that initiates the radical-based incorporation of methyl-derived carbide into the M cluster. The successful identification of NifB Ma and NifB Mt as functional homologs of NifB not only enabled classification of a new subset of radical SAM methyltransferases that specialize in complex metallocluster assembly, but also provided a new tool for further characterization of the distinctive, NifB-catalyzed methyl transfer and conversion to an iron-bound carbide.