Polypeptide chain ligation

The structure of PaFd was the first to be crystallographically determined (Adman et ai, 1973). The basic fold of the protein may be described as a pair of two stranded antiparallel )3 sheets. The two 4Fe 4S clusters are sandwiched between these /3 strands on one side and several helical segments on the other side. The clusters are packed in a predominantly hydrophobic environment. The internal sequence homology is clearly reflected in the structure the two clusters and much of the polypeptide chain are related by an approximate internal twofold rotation axis. The two clusters are ligated by the two sets of four cysteines in the two halves of the molecule. Surprisingly, each cluster is liganded by cysteines from both halves of the sequence, rather than cysteines from only one half (which are adjacent in the sequence). Cluster 1 is coordinated by Cys-8, -11, and -14 in the amino-terminal half and Cys-45 of the carboxy-terminal half, while cluster 2 is coordinated by Cys-35, -38, and -41 of the carboxy-terminal half and Cys-18 of the amino-terminal half. 

Nature often uses cystine knots of variable complexity to assemble polypeptide chains in the correct order and to stabilize the structure of the resulting proteins. Classical examples are proteins of the extracellular matrix with collagens and gelatines as the main components. This simple cystine-knot approach has been applied to synthetic constructs to ligate in a desired order helix bundles. [166 170 194-1%] It has also been used to mimic natural multiple-chain containing proteins like collagen.[83 1691971... 

Most known multiheme cytochromes and enzymes belong to the family of cytochromes c (see Iron Heme Proteins Electron Transport), which contain Fe-protoporphyrin IX covalently attached to the polypeptide chain by two thioether bonds, formed by addition of two cysteinyl residues to the vinyl side-chains of the porphyrin ring. The two cysteines form a characteristic amino acid sequence motif CXXCH, usually indicative of heme c ligation, and where the histidine is the axial fifth ligand to the iron. For some cytochromes (see Section 2), the number of residues between the two cysteines can be three or four. The heme redox potentials in cytochromes c cover a wide range and are tuned by several factors, usually dominated by the type of axial ligation and the extent of solvent exposure of the heme. ... 

Fig. 3, Ribbon drawings of the polypeptide chains in the M and L subunits of the Rp. viridis reaction center, redrawn from Deisenhofer et al. [102]. The drawings are oriented so that the normal to the chromatophore membrane is approximately vertical, with the periplasmic side of the membrane at the top and the cytoplasmic side at the bottom. The amino-terminal ends of the chains are on the cytoplasmic side of the membrane that of the L subunit is labeled 1. The five transmembrane helices are labeled A-E. In each subunit, the histidine residue that ligates one of the BChls of P is located near the top of helix D, on the periplasmic side of the hydrophobic region. The L and M subunits are closely appressed in the reaction center complex, so that the two BChls of P overlap (Fig. 4). The histidine ligands of the nonheme Fe are located toward the cytoplasmic ends of helices D and E in each subunit the glutamyl ligand in the M subunit is in the connecting region between D and E.

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