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PDBsum entry 4fxc
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Electron transport
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PDB id
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4fxc
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Contents |
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* Residue conservation analysis
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J Biochem (tokyo)
117:1017-1023
(1995)
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PubMed id:
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Tertiary structure of [2Fe-2S] ferredoxin from Spirulina platensis refined at 2.5 A resolution: structural comparisons of plant-type ferredoxins and an electrostatic potential analysis.
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K.Fukuyama,
N.Ueki,
H.Nakamura,
T.Tsukihara,
H.Matsubara.
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ABSTRACT
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The structure of plant-type [2Fe-2S] ferredoxin isolated from Spirulina
platensis has been refined using diffraction data to 2.5 A resolution by
alternate cycles of simulated annealing and manual revision of the model. The
final R factor is 19.9% for 2,912 reflections with F > 2 sigma F between 8.0
and 2.5 A resolution. S. platensis ferredoxin, like other plant-type [2Fe-2S]
ferredoxins, has a major alpha-helix flanking a sheet consisting of four beta
strands. The present refinement revises the conformation of residues 56-71, in
which a one-turn helix was identified. Superposition of the Spirulina ferredoxin
structure on the structures of other ferredoxins that have been well refined
showed structural perturbation at a few residues on the amino and carboxyl
termini and the turn between the first and second beta-strands. The
root-mean-square deviations of the corresponding C alpha atoms of the pairs of
ferredoxins range from 0.90 to 1.17 A for all the residues, but from 0.64 to
0.70 A if the few perturbed residues are excluded. Therefore, it may be
concluded that the main-chain foldings of all the plant-type [2Fe-2S]
ferredoxins are essentially the same. Electrostatic potential analysis showed
that the molecular surface around the cluster is negatively charged, whereas
that of the beta-sheet of the other side is positively charged. The interaction
between ferredoxin and ferredoxin-NADP+ reductase is discussed on the basis of
the charge distributions of these molecules and biochemical data.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Yamaoka,
Y.Ozawa,
Y.Ueno,
T.Endo,
Y.Morimoto,
A.Urushiyama,
D.Ohmori,
and
T.Imai
(2011).
Cyanidioschyzon merolae ferredoxin: A high resolution crystal structure analysis and its thermal stability.
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FEBS Lett,
585,
1299-1302.
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R.Nechushtai,
H.Lammert,
D.Michaeli,
Y.Eisenberg-Domovich,
J.A.Zuris,
M.A.Luca,
D.T.Capraro,
A.Fish,
O.Shimshon,
M.Roy,
A.Schug,
P.C.Whitford,
O.Livnah,
J.N.Onuchic,
and
P.A.Jennings
(2011).
Allostery in the ferredoxin protein motif does not involve a conformational switch.
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Proc Natl Acad Sci U S A,
108,
2240-2245.
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PDB code:
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D.R.Kolling,
R.I.Samoilova,
A.A.Shubin,
A.R.Crofts,
and
S.A.Dikanov
(2009).
Proton environment of reduced Rieske iron-sulfur cluster probed by two-dimensional ESEEM spectroscopy.
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J Phys Chem A,
113,
653-667.
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S.A.Dikanov,
R.I.Samoilova,
R.Kappl,
A.R.Crofts,
and
J.Hüttermann
(2009).
The reduced [2Fe-2S] clusters in adrenodoxin and Arthrospira platensis ferredoxin share spin density with protein nitrogens, probed using 2D ESEEM.
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Phys Chem Chem Phys,
11,
6807-6819.
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M.Prudêncio,
and
M.Ubbink
(2004).
Transient complexes of redox proteins: structural and dynamic details from NMR studies.
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J Mol Recognit,
17,
524-539.
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I.Bertini,
C.Luchinat,
A.Provenzani,
A.Rosato,
and
P.R.Vasos
(2002).
Browsing gene banks for Fe2S2 ferredoxins and structural modeling of 88 plant-type sequences: an analysis of fold and function.
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Proteins,
46,
110-127.
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R.Morales,
M.H.Charon,
G.Kachalova,
L.Serre,
M.Medina,
C.Gómez-Moreno,
and
M.Frey
(2000).
A redox-dependent interaction between two electron-transfer partners involved in photosynthesis.
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EMBO Rep,
1,
271-276.
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J.K.Hurley,
J.T.Hazzard,
M.Martínez-Júlvez,
M.Medina,
C.Gómez-Moreno,
and
G.Tollin
(1999).
Electrostatic forces involved in orienting Anabaena ferredoxin during binding to Anabaena ferredoxin:NADP+ reductase: site-specific mutagenesis, transient kinetic measurements, and electrostatic surface potentials.
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Protein Sci,
8,
1614-1622.
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M.T.Bes,
E.Parisini,
L.A.Inda,
L.M.Saraiva,
M.L.Peleato,
and
G.M.Sheldrick
(1999).
Crystal structure determination at 1.4 A resolution of ferredoxin from the green alga Chlorella fusca.
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Structure,
7,
1201-1211.
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PDB code:
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C.Binda,
A.Coda,
A.Aliverti,
G.Zanetti,
and
A.Mattevi
(1998).
Structure of the mutant E92K of [2Fe-2S] ferredoxin I from Spinacia oleracea at 1.7 A resolution.
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Acta Crystallogr D Biol Crystallogr,
54,
1353-1358.
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PDB code:
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S.Schmitz,
M.Martínez-Júlvez,
C.Gómez-Moreno,
and
H.Böhme
(1998).
Interaction of positively charged amino acid residues of recombinant, cyanobacterial ferredoxin:NADP+ reductase with ferredoxin probed by site directed mutagenesis.
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Biochim Biophys Acta,
1363,
85-93.
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H.Nishida,
and
K.Miki
(1996).
Electrostatic properties deduced from refined structures of NADH-cytochrome b5 reductase and the other flavin-dependent reductases: pyridine nucleotide-binding and interaction with an electron-transfer partner.
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Proteins,
26,
32-41.
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M.Vidakovic,
and
J.P.Germanas
(1996).
Electrostatic effects in electron transfer reactions of [2Fe-2S] ferredoxins with inorganic reagents.
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Protein Sci,
5,
1793-1799.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
