Iron protein structure

B. Nitrogenase Molybdenum-Iron Protein Structural Description of the Nitrogenase Proteins... 

C. Nitrogenase Molybdenum-Iron Protein Structure Structures of the Metal Centers of Nitrogenase... 

Page, C. C., Moser, C. C., Chen, X. and Dutton, P. L, 1999, Natural engineering principles of electron tunneling in biological oxidation-reduction. Nature 402, 47 -52. Parisini, E., F. Capozzi, P. Lubini, V. Lamzin, C. Luchinat, and G. M. Sheldrick. 1999. Ab initio solution and refinement of two high potential iron protein structures at atomic resolution. Acta Crystallography D. 55, 1773-1784. 

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. 

Iron-sulphur proteins structural chemistry of their chromophores and related systems. R. Mason and J. A. Zubieta, Angew. Chem., Int. Ed. Engl., 1973,12, 390-399 (101). 

Three core oxidation states are known for protein-bound [Fe4-S4(S.Cys)4]3+ clusters as illustrated in Figure 2.9. Native proteins exhibit either the [Fe4-S4]2+ + or the [Fe4-S4]3+,2+ redox couple, with proteins involved in the latter couple being referred to historically as HiPIP (high-potential iron protein). The three oxidation states have not been traversed in one protein unless its tertiary structure is significantly perturbed. 

Rubrerythrin is the trivial name given to a family of non-haem iron proteins that have been isolated from a number of bacteria (Figure 6.2). The structure of the best characterized rubrerythrin, that from Desulfovibrio vulgaris, has been determined by... 

Rana, T.M., and Meares, C.F. (1991a) Iron chelate-mediated proteolysis protein structure dependence. J. Am. Chem. Soc. 113, 1859-1861. 

Kim, J. and D.C. Rees. Structural models for the metal centers in the nitrogenase molybdenum-iron protein. Science 257,1677-1682 (1992). 

By any sort of definition, turns are an important feature of protein structure. Kuntz (1972) found 45% of protein backbone in turns or loops Chou and Fasman (1977) found 32% of protein chain in turns (counting four residues per turn) and Zimmerman and Scheraga (1977b) found 24% of the nonhelical residues in turns (counting only the central dipeptide). There are also some particular proteins whose structure appears heavily dependent on turns Fig. 38 shows high-potential iron protein (Carter et ah, 1974), with the 17 turns in 85 residues indicated and their location at the surface evident. 

Fig. 105. Examples of small disulfide-rich or metal-rich proteins (shown on the right side) compared with their more regular counterparts in other structural categories (shown at the left), (a) Tobacco mosaic virus protein, an up-and-down helix bundle (b) cytochrome bs, a distorted up-and-down helix bundle (c) trypsin domain 1, a Greek key antiparallel /3 barrel (d) high-potential iron protein, a distorted Greek key /3 barrel (e) glutathione reductase domain 3, an open-face sandwich fi sheet (f) ferredoxin, a distorted open-face sandwich f) sheet.

The coordination sphere around the ferrous iron center is almost octahedral with the heteroscorpionate clamp causing a deviation of 4-6° from the ideal 90° angle. A comparison with very high-resolution protein structures such as IPNS or CAS clearly shows a good correspondence of structure 4b in distances and angles with the active sites of the non-heme iron enz5unes (Table I). 

The iron enzymes catalase and peroxidasepromote these reactions very effectively, but it is unlikely that both reactants are coordinated to the metal during the reaction. It is generally true that the metal site is restricted in enzymes, allowing coordination of only one reactant. The other reactant is however often held close by the protein structure. 

Cytochromes are electron-transfer proteins having one or several haem groups. Cytochrome c binds to the protein by one or, more commonly two, thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. Cytochrome c has been proved to be a useful model system for studying the relationship between protein structure and thermostability due to the availability of its three-dimensional structure from a wide variety of organisms, both mesophiles and thermophiles. 

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