Flavodoxin structure

Figure 8 Illustration of the ensemble of 10 E. coli Flavodoxin structures obtained from homology modeling using distance geometry, superimposed on the crystal structure (heavy line) so as to minimize the coordinate differences to the alpha carbons in residues 4-170. Only the heavy backbone and aromatic sidechain atoms are shown, together with those of the flavin mononucleotide cofactor (lower left)...

Figure 1 The basis of comparative protein structure modeling. Comparative modeling is possible because evolution resulted in families of proteins, such as the flavodoxin family, modeled here, which share both similar sequences and 3D structures. In this illustration, the 3D structure of the flavodoxin sequence from C. crispus (target) can be modeled using other structures in the same family (templates). The tree shows the sequence similarity (percent sequence identity) and structural similarity (the percentage of the atoms that superpose within 3.8 A of each other and the RMS difference between them) among the members of the family.

Figure 2.11 Beta sheets are usuaiiy represented simply by arrows in topology diagrams that show both the direction of each (3 strand and the way the strands are connected to each other along the polypeptide chain. Such topology diagrams are here compared with more elaborate schematic diagrams for different types of (3 sheets, (a) Four strands. Antiparallel (3 sheet in one domain of the enzyme aspartate transcarbamoylase. The structure of this enzyme has been determined to 2.8 A resolution in the laboratory of William Lipscomb, Harvard University, (b) Five strands. Parallel (3 sheet in the redox protein flavodoxin, the structure of which has been determined to 1.8 A resolution in the laboratory of Martha Ludwig, University of Michigan, (c) Eight strands. Antiparallel barrel in the electron carrier plastocyanln. This Is a closed barrel where the sheet is folded such that (3 strands 2 and 8 are adjacent. The structure has been determined to 1.6 A resolution in the laboratory of Hans Freeman in Sydney, Australia. (Adapted from J. Richardson.)...

The first structure, flavodoxin (Figure 4.14a), has one such position, between strands 1 and 3. The connection from strand 1 goes to the right and that from strand 3 to the left. In the schematic diagram in Figure 4.14a we can see that the corresponding a helices are on opposite sides of the p sheet. The loops from these two p strands, 1 and 3, to their respective a helices form the major part of the binding cleft for the coenzyme FMN (flavin mononucleotide). 

In globular protein structures, it is common for one face of an a-helix to be exposed to the water solvent, with the other face toward the hydrophobic interior of the protein. The outward face of such an amphiphilic helix consists mainly of polar and charged residues, whereas the inward face contains mostly nonpolar, hydrophobic residues. A good example of such a surface helix is that of residues 153 to 166 of flavodoxin from Anabaena (Figure 6.24). Note that the helical wheel presentation of this helix readily shows that one face contains four hydrophobic residues and that the other is almost entirely polar and charged. 

This study of such of an electron transfer chain is most timely, since the 3D structures of all the components involved are known (and related components can easily be obtained by homology molecular modeling). Proposals of structural models for the complexes formed between D. gigas AOR and flavodoxin, based on the available X-ray... 

This review will not be concerned with functionally alternative structures and metabolites which appear in iron-limited growth. Thus Clostridium pasteurianum and other bacteria when grown in the presence of iron form ferredoxin grown at low iron the same organisms form flavodoxin, a flavoprotein [Knight, ., Jr., Hardy, R. W. J. Biol. Chem. 242, 1370 (1967) Mayhem, S. G., Massey, V. J. Biol. Chem. 244, 794 (1969)]. 

Fig. 23. Schematic drawing of the backbone of flavodoxin, a protein in which a parallel 0 sheet is the dominant structural feature. The sheet (represented by arrows) is shown from one edge, so that the characteristic twist can be seen clearly.

The doubly wound structures were first recognized as a category by Rossmann in comparing flavodoxin with lactate dehydrogenase dl. As more and more protein structures were solved which fell into this... 

The small subunit is composed of two domains. The N-terminal domain shows the characteristic architecture of flavodoxin with the phosphate moiety of the flavin cofactor occupying the binding pocket of the proximal [4Fe-4S] cluster. This N-terminal domain, including the proximal cluster, is found in all [NiFe] hydrogenases and is consequently an essential feature, both structural and functional, of these enzymes. By contrast, the C-terminal domain that binds the other [FeS] clusters is less organised and more variable in [FeS] cluster content and amino acid sequence. 

The tertiary structure of small subunit enzymes can be subdivided into four distinct regions, and the C-terminal or flavodoxin domain of the large subunit enzymes becomes a fifth region. These are indicated in Fig. 8 for clarity. The first region is the amino terminal arm (Fig. 8), which extends 50 or more residues from the amino terminus almost to the essential histidine residue (to residue 53 in PMC, 60 in PVC, 73 in BLC, and 127 in HPII). There is very little structural similarity in the N-terminal region and, in the case of HPII, the structure of the terminal 27 residues is not even defined and they do not appear in the crystal structure. Within the N-terminal arm is a 20-residue helix, helix a2 in HPII, which is the first secondary structure element common to all catalases. The presence of helix al varies among catalases, and there is no sequence or location equivalence even when it is present. 

In large subunit enzymes (PVC and HPII), a short segment of about 30 residues links the a-helical domain to the C-terminal domain (Fig. 8). The latter segment is a conspicuous addition to the small subunit containing about 150 residues folded into a structure that resembles flavodoxin. For example, there is a root mean square deviation of 3.0 A between flavodoxin and approximately 100 residues of the C-terminal domains of either HPII or PVC. This can be compared to the 1.8 A root mean square deviation for 134 centers between the C-terminal domains of HPII and PVC. Unlike the N-terminal end, the final C-terminal residue Ala753 is visible in the structure of HPII. The C-terminal domain contains extensive secondary structure in the form of four a-helices (al5-18) and eight fi-strands (fi9-16). Despite the obvious structural similarity to flavodoxin, there is no evidence of nucleotide binding in the domain and its function remains a mystery. 

In plants, algae and cyanobacteria the light-induced charge separation of photosynthesis occurs in 2 large membrane proteins, called photosystem (PS) I and II. PS I catalyzes the ET from plastocyanin (or cytochrome c6) on the luminal side to ferrodoxin (or flavodoxin) on the stromal side of the membrane (for review see reference 177). PS I from the cyanobacterium Thermo(Y13)synechococcus (T.) elongatus was crystallized and an X-ray crystallographic structure at 2.5 A resolution has recently been obtained.18,178 Very recently, the structure from plant PS I has also been reported with a resolution of 4.4 A.179... 

The three-dimensional structures, or part of it, are also known for Desulfovibrio vulgaris and Anacystis nidulans flavodoxins. These results, including those obtained on C.MP., were recently summarized by Adman . Hence, these results will be discussed only briefly. The x-ray structures show that the isoalloxazine ring is embedded in a hydrophobic pocket of the apoprotein, i.e. flanked by at least one aromatic amino acid residue. During the redox transitions, especially from the oxidized to the semiquinone state, small conformational changes occur and contacts with the isoalloxazine ring are formed or broken. These conformational transitions form probably a kinetic barrier so that the semiquinone state is trapped by the apoprotein and, therefore, rather stable towards oxidation by molecular oxygen. 

Smith, W. W., Ludwig, M. L., Pattridge, K. A., Tsemoglou, D., Petsko, G. A. Crystallographic Studies of Flavodoxins Some correlation between structure and redox potential. In Frontiers of Biol. Energetics, Vol. II (Dutton, P. L., Leigh, J. S. Scarpa, A. eds.) pp. 957-964. New York, San Francisco, London, Academic Press 1978... 

Watenpaugh, K. D., Sieker, L. C., Jensen, L. H. A crystallographic structural study of the oxidation states of Desulfovibrio vulgaris flavodoxin. In Flavins and flavoproteins (Singer, T. P. ed.) pp. 405-410. Amsterdam, Elsevier 1976... 

The soluble electron carriers released from the reaction centers into the cytoplasm of bacteria or into the stroma of chloroplasts are reduced single-electron carriers. Bacterial ferredoxin with two Fe4S4 clusters is formed by bacteria if enough iron is present. In its absence flavodoxin (Chapter 15), which may carry either one or two electrons, is used. In chloroplasts the carrier is the soluble chloroplast ferredoxin (Fig. 16-16,C), which contains one Fe2S2 center. Reduced ferredoxin transfers electrons to NADP+ (Eq. 15-28) via ferredoxin NADP oxidoreductase, a flavoprotein of known three-dimensional structure.367 369... 

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