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PDBsum entry 2c8v
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Oxidoreductase
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PDB id
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2c8v
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References listed in PDB file
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Key reference
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Title
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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.
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Authors
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S.Sen,
A.Krishnakumar,
J.Mcclead,
M.K.Johnson,
L.C.Seefeldt,
R.K.Szilagyi,
J.W.Peters.
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Ref.
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J Inorg Biochem, 2006,
100,
1041-1052.
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PubMed id
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Abstract
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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.
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