Ferredoxins structure

Fe-xS] ferredoxins, 33 54-55 rubredoxin, 33 44-51 hydrophobic effect, 33 60-62 significance, 33 40-44 metal complexes of, 7 218-220 model complexes, catalysis by, 33 61-62 Peptococcus aerogenes ferredoxin, structure, 38 242, 244-245... 

Fig. 9. Three dimensionai structure of ferredoxin from Pseudomonas aerogenes [the portion without the black ribbons] determined by X-ray crystallography at 2.8 A resolution. The additional amino-acid residues contained in PsaC protein are added to the P. aerogenes ferredoxin backbone at the C-terminus and inserted at position 22 to model the structure of the PsaC protein. P. aerogenes ferredoxin structure from Adman, Sieker and Jensen (1973) The structure of bacterial ferredoxin. J Biol Chem 248 3993,...

VJ Fig. 28.14 The iron-sulfur units from ferredoxins, structurally characterized by X-ray diffraction (a) the [2Fe-2S]... 

Fig. 29.15 The iron-sulfur units from ferredoxins, structurally characterized by X-ray diffraction (a) the [2Fe-2S] ferredoxin from spinach (Spinacia oleraced), (b) the [3Fe-4S] ferredoxin from the bacterium Azotobacter vinelandii, and (c) the [4Fe-4S] ferredoxin from the bacterium Chromatium vinosum. Hydrogen atoms are omitted colour code Fe, green S, yellow C, grey.

Figure 8.39 Fourier transformed Fe extended X-ray absorption fine structure (EXAFS) and retransformation, after applying a 0.9-3.5 A filter window, of (a) a rubredoxin, (b) a plant ferredoxin and (c) a bacterial ferredoxin, whose structures are also shown. (Reproduced, with permission, Ifom Teo, B. K. and Joy, D. C. (Eds), EXAFS Spectroscopy, p. 15, Plenum, New York, 1981)...

A second example is that of an Ala-to-Cys mutation, which causes the fonnation of a rare SH S hydrogen bond between the cysteine and a redox site sulfur and a 50 mV decrease in redox potential (and vice versa) in the bacterial ferredoxins [73]. Here, the side chain contribution of the cysteine is significant however, a backbone shift can also contribute depending on whether the nearby residues allow it to happen. Site-specific mutants have confirmed the redox potential shift [76,77] and the side chain conformation of cysteine but not the backbone shift in the case with crystal structures of both the native and mutant species [78] the latter can be attributed to the specific sequence of the ferre-doxin studied [73]. 

Nonrepetitive but well-defined structures of this type form many important features of enzyme active sites. In some cases, a particular arrangement of coil structure providing a specific type of functional site recurs in several functionally related proteins. The peptide loop that binds iron-sulfur clusters in both ferredoxin and high potential iron protein is one example. Another is the central loop portion of the E—F hand structure that binds a calcium ion in several calcium-binding proteins, including calmodulin, carp parvalbumin, troponin C, and the intestinal calcium-binding protein. This loop, shown in Figure 6.26, connects two short a-helices. The calcium ion nestles into the pocket formed by this structure. 

In this work we examine the low energy UV-visible absorption spectrum of the [Fe2 ft - S2) P o- 61148) )2] complex, Figure 1, whose synthesis, structure, and properties have recently been reported. The complex contains a [Fe — S — S - Fe] core and is a structural isomer of the 2-Fe [Fe — ill — 8)2 — Fe ferredoxin. The electronic structure of the disulfide complex is, however, unknown, and can be associated with either an antifer-romagnetically (AF) coupled [Fe d ) - - Fe d )] system, or with a... 

In an earlier work, we have proposed a theoretical procedure for the spectroscopy of antiferromagnetically (AF) coupled transition-metal dimers and have successfully applied this approach to the electronic absorption spectrum of model 2-Fe ferredoxin. In this work we apply this same procedure to the [Fe2in - 82) P o - CeH48)2)2 complex in order to better understand the electronic structure of this compound. As in our previous work" we base our analysis on the Intermediate Neglect of the Differential Overlap model parameterized for spectroscopy (INDO/S), utilizing a procedure outlined in detail in Reference 4. 

Only a few residues show more than 75% sequence identity, including four glycine residues, a proline residue at the beginning of the Pro loop, and a phenylalanine residue in a position corresponding to the conserved residue Tyr 165 of the bovine heart Rieske protein. However, structure prediction and sequence comparison with Rieske proteins from bci complexes suggests that the fold will be very similar in all Rieske-type ferredoxins, as in the other Rieske or Rieske-type proteins (see Section III,B,1). 

NMR spectra have been reported for the Rieske-type ferredoxins from Xanthobacter strain Py2 (88) and of toluene 4-monooxygenase from Pseudomonas mendocina (T4MOC) (88a) as well as for the water-soluble Rieske fragment from the bci complex of Paracoccus deni-trificans (ISFpd) (89). The spectra of these proteins are similar, which is consistent with the close structural relationship between the three proteins. In the reduced (paramagnetic) state, all three proteins show several hyperfine-shifted resonances between +83 and -16 ppm at 400 MHz or between 110 and +25 ppm at 300 MHz (Table X). 

The structure of phthalate dioxygenase reductase that transfers electrons directly from NADPH to phthalate dioxygenase has been determined by X-ray crystallography (119). In class II or class III dioxygenases, the ferredoxin obligately transfers electrons from the reductase to the terminal dioxygenase (64a) it can be either a Rieske-type ferredoxin or a ferredoxin containing a 4-cysteine coordinated [2Fe-2S] cluster. 

It appears that Cluster C catalyzes the chemistry of CO oxidation and transfers electrons to Cluster B, which donates electrons to external acceptors such as ferredoxin. Since a crystal structure of this protein does not exist, the proposed structure of Cluster C is based on spectroscopic measurements. In some cases, the EPR spectrum of a metal center is diagnostic of the type of center. However, the EPR spectra of Cluster C are unusual. The paramagnetic states of Cluster C (Credi and Cred2) have g-values that are atypical of standard [4Fe-4S] clusters (Table III) and are similar to those in a variety of structurally unrelated systems including a t-oxo bridged ion dimer), a [Fe4S4] ... 

Fig. 2. Protein backbone representations of (a) the 2[4Fe-4S] ferredoxin from Peptococcus aerogenes, (b) the proposed structure of the FA/FB-binding protein of PSl based on the 4 A crystsd structure (25), and (c) the [3Fe-4S][4Fe-4S] ferredoxin from Sulfolo-bus acidocaldarius. Ligands to clusters Fa and Fb, important residues as well as the loop extension (see text) EU e highlighted in darker gray.

Fig. 3. Sequence comparison of the FA/FB-binding subunits of PSl from tobacco and the RC of green sulfur bacteria with that of the 2[4Fe-4S] ferredoxin from Peptococcus aerogenes. Cysteine ligands to the right-hand cluster in the three structures of Fig. 2 (i.e., cluster Fb for the case of the FA/FB-protein) are marked by open boxes Emd residues ligating the left-hand cluster by hatched boxes.

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