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PDBsum entry 2nip
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References listed in PDB file
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Key reference
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Title
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Conformational variability in structures of the nitrogenase iron proteins from azotobacter vinelandii and clostridium pasteurianum.
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Authors
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J.L.Schlessman,
D.Woo,
L.Joshua-Tor,
J.B.Howard,
D.C.Rees.
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Ref.
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J Mol Biol, 1998,
280,
669-685.
[DOI no: ]
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PubMed id
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Abstract
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The nitrogenase iron (Fe) protein performs multiple functions during biological
nitrogen fixation, including mediating the mechanistically essential coupling
between ATP hydrolysis and electron transfer to the nitrogenase molybdenum iron
(MoFe) protein during substrate reduction, and participating in the biosynthesis
and insertion of the FeMo-cofactor into the MoFe-protein. To establish a
structural framework for addressing the diverse functions of Fe-protein, crystal
structures of the Fe-proteins from Azotobacter vinelandii and Clostridium
pasteurianum have been determined at resolutions of 2.2 A and 1.93 A,
respectively. These two Fe-proteins are among the more diverse in terms of amino
acid sequence and biochemical properties. As described initially for the A.
vinelandii Fe-protein in a different crystal form at 2.9 A resolution, each
subunit of the dimeric Fe-protein adopts a polypeptide fold related to other
mononucleotide-binding proteins such as G-proteins, with the two subunits
bridged by a 4Fe:4S cluster. The overall similarities in the subunit fold and
dimer arrangement observed in the structures of the A. vinelandii and C.
pasteurianum Fe-proteins indicate that they are representative of the
conformation of free Fe-protein that is not in complex with nucleotide or the
MoFe-protein. Residues in the cluster and nucleotide-binding sites are linked by
a network of conserved hydrogen bonds, salt-bridges and water molecules that may
conformationally couple these regions. Significant variability is observed in
localized regions, especially near the 4Fe:4S cluster and the MoFe-protein
binding surface, that change conformation upon formation of the ADP.AlF4-
stabilized complex with the MoFe-protein. A core of 140 conserved residues is
identified in an alignment of 59 Fe-protein sequences that may be useful for the
identification of homologous proteins with functions comparable to that of
Fe-protein in non-nitrogen fixing systems.
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Figure 4.
Figure 4. (a) A representation of one Fe-protein monomer colored according to rms deviation in C
a
position, follow-
ing superposition of the four AV2 and CP2 subunits. Residues with high rms deviation, such as the C terminus, are
indicated in red; regions of strong structural conservation, such as the b-sheet, are indicated in dark blue. (b) A rep-
resentation of one Fe-protein monomer colored according to amino acid residue conservation, following alignment of
59 Fe-protein sequences. Residues in red, such as the C terminus, indicate the regions of greatest sequence variability;
those in dark blue, such as the 4Fe:4S cluster ligands, P-loop, Switch I and Switch II residues, indicate regions of
strongest sequence conservation. In both (a) and (b), the view is from the dimer interface, and Av2 residue numbers
are included for reference.
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Figure 6.
Figure 6. Structural variability in the subunit-subunit interactions near the 4Fe:4S clusters of CP2 and AV2. Subunit
A of each protein is shown in red, and subunit B in green. The 4Fe:4S cluster atoms are colored as in Figure 2. Comp-
lementary residues on the opposing subunits have been omitted for ease of viewing. (a) Three intersubunit hydrogen
bonds are located near the 4Fe:4S cluster in CP2. (b) Crystal packing forces distort this region in AV2, with the loss
of several of these intersubunit interactions. The C terminus of a neighboring molecule (shown in cyan) forms two
hydrogen bonds with the 4Fe:4S region of subunit A in AV2 at residues Gly96 and Cys97. Despite this conformation-
al alteration near the 4Fe:4S cluster in subunit A, the corresponding region in subunit B is undisturbed.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
280,
669-685)
copyright 1998.
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