8Q50

Nitrogenase Fe protein from Methanothermococcus thermolithotrophicus, tetragonal crystalline form at 1.91-A resolution

Summary for 8Q50

• Entry DOI: 10.2210/pdb8q50/pdb
• Descriptor: Nitrogenase iron protein 1, CALCIUM ION, FE2/S2 (INORGANIC) CLUSTER, ... (6 entities in total)
• Functional Keywords: nitrogenase, electron donor, atpase, [4fe-4s]-cluster, electron transfer, conformational changes, methanogenic archaea, oxidoreductase, o2-sensitivity, n2-fixation, electron transport
• Biological source: Methanothermococcus thermolithotrophicus DSM 2095
• Total number of polymer chains: 1
• Total formula weight: 31849.08

Authors

Maslac, N.,Wagner, T. (deposition date: 2023-08-07, release date: 2024-05-15, Last modification date: 2024-08-14)

Primary citation

Maslac, N.,Cadoux, C.,Bolte, P.,Murken, F.,Gu, W.,Milton, R.D.,Wagner, T.
Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales.
Febs J., 291:3454-3480, 2024

PubMed Abstract: The nitrogenase reductase NifH catalyses ATP-dependent electron delivery to the Mo-nitrogenase, a reaction central to biological dinitrogen (N) fixation. While NifHs have been extensively studied in bacteria, structural information about their archaeal counterparts is limited. Archaeal NifHs are considered more ancient, particularly those from Methanococcales, a group of marine hydrogenotrophic methanogens, which includes diazotrophs growing at temperatures near 92 °C. Here, we structurally and biochemically analyse NifHs from three Methanococcales, offering the X-ray crystal structures from meso-, thermo-, and hyperthermophilic methanogens. While NifH from Methanococcus maripaludis (37 °C) was obtained through heterologous recombinant expression, the proteins from Methanothermococcus thermolithotrophicus (65 °C) and Methanocaldococcus infernus (85 °C) were natively purified from the diazotrophic archaea. The structures from M. thermolithotrophicus crystallised as isolated exhibit high flexibility. In contrast, the complexes of NifH with MgADP obtained from the three methanogens are superposable, more rigid, and present remarkable structural conservation with their homologues. They retain key structural features of P-loop NTPases and share similar electrostatic profiles with the counterpart from the bacterial model organism Azotobacter vinelandii. In comparison to the NifH from the phylogenetically distant Methanosarcina acetivorans, these reductases do not cross-react significantly with Mo-nitrogenase from A. vinelandii. However, they associate with bacterial nitrogenase when ADP· is added to mimic a transient reactive state. Accordingly, detailed surface analyses suggest that subtle substitutions would affect optimal binding during the catalytic cycle between the NifH from Methanococcales and the bacterial nitrogenase, implying differences in the N-machinery from these ancient archaea.

PubMed: 38696373
DOI: 10.1111/febs.17148

Experimental method

X-RAY DIFFRACTION (1.91 Å)