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PDBsum entry 1m2a
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Electron transport
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PDB id
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1m2a
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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High resolution crystal structures of the wild type and cys-55-->Ser and cys-59-->Ser variants of the thioredoxin-Like [2fe-2s] ferredoxin from aquifex aeolicus.
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Authors
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A.P.Yeh,
X.I.Ambroggio,
S.L.Andrade,
O.Einsle,
C.Chatelet,
J.Meyer,
D.C.Rees.
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Ref.
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J Biol Chem, 2002,
277,
34499-34507.
[DOI no: ]
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PubMed id
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Abstract
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ferredoxin (Fd4) from Aquifex aeolicus adopts a thioredoxin-like
ferredoxins. Crystal
structures of the Cys-55 --> Ser (C55S) and Cys-59 --> Ser (C59S) variants of
this protein have been determined to 1.25 A and 1.05 A resolution, respectively,
whereas the resolution of the wild type (WT) has been extended to 1.5 A. The
cluster,
cluster-containing protein, namely, pronounced distortions in the cysteine
coordination to the cluster and a Calpha-H-Sgamma hydrogen bond between cluster
ligands Cys-55 and Cys-9. These features may contribute to the unusual
clusters in WT and variants
of this ferredoxin. The structures of the two variants of Fd4, in which single
cluster are replaced by serine, establish the
metric details of serine-ligated Fe-S active sites with unprecedented accuracy.
Both the cluster and its surrounding protein matrix change in subtle ways to
accommodate this ligand substitution, particularly in terms of distortions of
the Fe(2)S(2) inorganic core from planarity and displacements of the polypeptide
chain. These high resolution structures illustrate how the interactions between
polypeptide chains and Fe-S active sites reflect combinations of flexibility and
rigidity on the part of both partners; these themes are also evident in more
complex systems, as exemplified by changes associated with serine ligation of
the nitrogenase P cluster.
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Figure 3.
Fig. 3. A, stereoview of the [2Fe-2S] cluster and its
ligands from the WT ( cyan), C55S (yellow), and C59S (purple)
structures upon superposition of the corresponding 101 C  atoms of
the three structures, showing the varying degree of positional
shifts that occur in the inorganic core as well as residues 55
and 59 caused by the cysteine to serine substitutions. B,
stereoview of the same region, viewed from a direction
perpendicular to that in A, illustrates the varying degrees to
which the inorganic core is distorted in each structure. The
color scheme is the same as in A.
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Figure 4.
Fig. 4. Stereoview comparing the P cluster of nitrogenase
in the oxidized (transparent ball-and-stick model in cyan) and
reduced (solid ball-and-stick model in gray) states (39, 40). In
the oxidized state, one of the irons is coordinated by the side
chain of Ser-  188, whereas
in the reduced state this iron is shifted and coordinates an
inorganic sulfur in the cluster instead. The coloring scheme is
as in Fig. 3. PDB entries 2MIN (oxidized) and 3MIN (reduced)
were used for this figure.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
34499-34507)
copyright 2002.
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Secondary reference #1
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Title
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Structure of a thioredoxin-Like [2fe-2s] ferredoxin from aquifex aeolicus.
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Authors
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A.P.Yeh,
C.Chatelet,
S.M.Soltis,
P.Kuhn,
J.Meyer,
D.C.Rees.
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Ref.
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J Mol Biol, 2000,
300,
587-595.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Stereoview of the superposition of
Anabaenathioredoxin-2 (orange) [Saarinen et al 1995] and a
monomer of AaFd4 (green), showing the similarity between the
folds. In addition to the similarity of the overall folds, two
of the [2Fe-2S] cysteine ligands, Cys9 and Cys22 (shown in a
darker shade of green), in AaFd4 are positioned near the two
active site cysteine residues of thioredoxin-2, Cys32 and Cys35
(shown in a darker shade of orange).
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Figure 4.
Figure 4. (a) Stereoview of the immediate environment
around the [2Fe-2S] cluster. The color scheme for the [2Fe-2S]
cluster is the same as in Figure 2. Potential hydrogen bonds
between the cluster sulfide S1 atom and the amide nitrogen atom
of Cys22 and the guanidinium group of Arg 13 and between the
cluster sulfide S2 atom and the amide nitrogen atoms of Met56,
Asn57, Ala58, and Cys59 are shown as broken lines. (b)
Stereoview of the [2Fe-2S] cluster and nearby residues
corresponding to ones in CpFd which, when replaced by cysteine,
can serve as alternative ligands to the [2Fe-2S] cluster. Cys 22
and Cys 59, the two cysteine ligands which can be replaced (Cys
24 and Cys 60 in CpFd), are shown in cyan. Cysteine residues
introduced into the polypeptide chain between residues 12-24
(represented in purple) can serve as a cluster ligand in place
of Cys 24, while a cysteine residue substituted for Gln 19
(pink) can replace Cys 60 as a ligand.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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