Cofactor ligation

The first etCCR application has been reported for a partially C— N-labeled phosphotyrosine peptide derived from interleukin-4 receptor ligated to STAT-6 [107] and subsequent studies involve nucleotide cofactors ligated to human recombinant deoxycytidine kinase [108] and epothilone A bound to tubulin [109]. Since etCCR usually involves isotope-labeling schemes for the ligand, its applicability is limited to specific molecular classes. 

Fig. 4. Structure of the iron molybdenum cofactor, FeMoco (after Chan, Kim, and Rees, (4) Bolin et al. (5) and Mayer et al. (7)). The FeMoco is ligated, within the a subunits of the a2j82 tetrameric structure, by residues Hisa442 and Cysa275 (Avl residue numbers).

Homocitrate is bound to the molybdenum atom by its 2-carboxy and 2-hydroxy groups and projects down from the molybdenum atom of the cofactor toward the P clusters. This end of FeMoco is surrounded by several water molecules (5, 7), which has led to the suggestion that homocitrate might be involved in proton donation to the active site for substrate reduction. In contrast, the cysteine-ligated end of FeMoco is virtually anhydrous. 

The molyhdopterin cofactor, as found in different enzymes, may be present either as the nucleoside monophosphate or in the dinucleotide form. In some cases the molybdenum atom binds one single cofactor molecule, while in others, two pterin cofactors coordinate the metal. Molyhdopterin cytosine dinucleotide (MCD) is found in AORs from sulfate reducers, and molyhdopterin adenine dinucleotide and molyb-dopterin hypoxanthine dinucleotide were reported for other enzymes (205). The first structural evidence for binding of the dithiolene group of the pterin tricyclic system to molybdenum was shown for the AOR from Pyrococcus furiosus and D. gigas (199). In the latter, one molyb-dopterin cytosine dinucleotide (MCD) is used for molybdenum ligation. Two molecules of MGD are present in the formate dehydrogenase and nitrate reductase. 

A relationship between the redox state of an iron—sulfur center and the conformation of the host protein was furthermore established in an X-ray crystal study on center P in Azotobacter vinelandii nitroge-nase (270). In this enzyme, the two-electron oxidation of center P was found to be accompanied by a significant displacement of about 1 A of two iron atoms. In both cases, this displacement was associated with an additional ligation provided by a serine residue and the amide nitrogen of a cysteine residue, respectively. Since these two residues are protonable, it has been suggested that this structural change might help to synchronize the transfer of electrons and protons to the Fe-Mo cofactor of the enzyme (270). 

Figure 18.4 Structures of heme/Cu oxidases at different levels of detail, (a) Position of the redox-active cofactors relative to the membrane of CcO (left, only two obligatory subunits are shown) and quinol oxidase (right), (b) Electron transfer paths in mammalian CcO. Note that the imidazoles that ligate six-coordinate heme a and the five-coordinate heme are linked by a single amino acid, which can serve as a wire for electron transfer from ferroheme a to ferriheme as. (c) The O2 reduction site of mammalian CcO the numbering of the residues corresponds to that in the crystal structure of bovine heart CcO. The subscript 3 in heme as and heme 03 signifies the heme that binds O2. The structures were generated using coordinates deposited in the Protein Data Bank, lari [Ostermeier et al., 1997] Ifft [Abramson et al., 2000] (a) and locc [Tsukihara et al., 1996] (b, c).

Figure 18.5 Plausible sequence of steps responsible for rapid and selective reduction of O2 to H2O by mixed-valence CcO. The square frames signify the catalytic site (Fig. 18.4c) imidazole ligation of Cub is omitted for clarity in some or aU intermediates, Cub may additionally be ligated by an exogenous ligand, such as H2O (in Cu ) or OH (in Cu ) such ligation is not established, and hence is omitted in all but compound Pm and the putative hydroperoxo intermediate. The dashed frames signify the noncatalytic redox cofactors. Typically used phenomenological names of the spectroscopically observed intermediates (compounds A, E, H, etc.) are also indicated.

In contrast to the use of self-assembly reactions and metal ion coordination preferences to direct the construction of mixed cofactor systems, the use of SPPS or selective chemical ligation allows for the direct covalent attachment of cofactors for the construction of mixed cofactor systems within de novo design. Figure 11 shows the flavocy-tochrome maquette constructed by Dutton and co-workers (149) using a flavin moiety covalently attached to a unique cysteine residue inside a four helix bundle with bis-histidine binding sites for heme... 

The FeMo-co or M center of the FeMo protein has been identified spectroscoplcally(, 13,30) within the protein and has been extracted from the protein into N-methyl formamlde(31) and other organic solvents(32.33). Its biochemical authenticity can be assayed by its ability to activate FeMo protein from a mutant organism that produces protein that lacks the M center(31). The extracted cofactor resembles the M-center unit spectroscopically and structurally as shown in Table I. It seems reasonable to presume that the differences are due to variation in the ligation of the center between the protein and the organic solvent(34). 

Important The active center of a protein and the binding site to its ligate has to be protected by substrate, cofactor, ligand, or their analogue during coupling to the chromatographic support. 

The electrochemistry of the extracted FeMo cofactor has also been studied in depth [20]. Extracted At-methyl formamide (NMF) solutions of FeMo-co contain the intact cluster, probably with retention of the exogenous homocitrate ligand. Protein ligation are replaced with NMF ligands at... 

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