2C8V

Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP

Summary for 2C8V

• Entry DOI: 10.2210/pdb2c8v/pdb
• Related: 1DE0 1FP6 1G1M 1G20 1G21 1G5P 1M1Y 1M34 1N2C 1NIP 1RW4 1XCP 1XD8 1XD9 1XDB 2AFH 2AFI 2AFK 2NIP
• Descriptor: NITROGENASE IRON PROTEIN 1, FE2/S2 (INORGANIC) CLUSTER, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: oxidoreductase, nitrogenase, nitrogen fixation, mgadp, fe protein, av2, 4fe- 4s, atp-binding, iron, iron-sulfur, metal-binding, nucleotide-binding
• Biological source: AZOTOBACTER VINELANDII
• Total number of polymer chains: 1
• Total formula weight: 32187.02

Authors

Sen, S.,Krishnakumar, A.,McClead, J.,Johnson, M.K.,Seefeldt, L.C.,Szilagyi, R.K.,Peters, J.W. (deposition date: 2005-12-08, release date: 2006-06-01, Last modification date: 2024-05-08)

Primary citation

Sen, S.,Krishnakumar, A.,Mcclead, J.,Johnson, M.K.,Seefeldt, L.C.,Szilagyi, R.K.,Peters, J.W.
Insights Into the Role of Nucleotide-Dependent Conformational Change in Nitrogenase Catalysis: Structural Characterization of the Nitrogenase Fe Protein Leu127 Deletion Variant with Bound Mgatp.
J.Inorg.Biochem., 100:1041-, 2006

PubMed Abstract: In the present work, determination of the structure of the nitrogenase Leu 127 deletion variant Fe protein with MgATP bound is presented, along with density functional theory calculations, to provide insights into the roles of MgATP in the nitrogenase reaction mechanism. Comparison of the MgATP-bound structure of this Fe protein to the nucleotide-free form indicates that the binding of MgATP does not alter the overall structure of the variant significantly with only small differences in the conformation of amino acids in direct contact with the two bound MgATP molecules being seen. The earlier observation of splitting of the [4Fe-4S] cluster into two [2Fe-2S] clusters was observed to be unaltered upon binding MgATP. Density functional theory was used to probe the assignment of ligands to the two [2Fe-2S] rhombs. The Mg(2+) environment in the MgATP-bound structure of the Leu127 deletion Fe protein is similar to that observed for the Fe protein in the nitrogenase Fe protein: MoFe protein complex stabilized by MgADP and tetrafluoroaluminate suggesting that large scale conformational change implicated for the Fe protein may not be mediated by changes in the Mg(2+) coordination. The results presented here indicated that MgATP may enhance the stability of an open conformation and prohibit intersubunit interactions, which have been implicated in promoting nucleotide hydrolysis. This could be critical to the tight control of MgATP hydrolysis observed within the nitrogenase complex and may be important for maintaining unidirectional electron flow toward substrate reduction.

PubMed: 16616373
DOI: 10.1016/J.JINORGBIO.2006.02.016

Experimental method

X-RAY DIFFRACTION (2.5 Å)