Homocitrate

Iron Sulfur Compounds. Many molecular compounds (18—20) are known in which iron is tetrahedraHy coordinated by a combination of thiolate and sulfide donors. Of the 10 or more stmcturaHy characterized classes of Fe—S compounds, the four shown in Figure 1 are known to occur in proteins. The mononuclear iron site REPLACE occurs in the one-iron bacterial electron-transfer protein mbredoxin. The [2Fe—2S] (10) and [4Fe—4S] (12) cubane stmctures are found in the 2-, 4-, and 8-iron ferredoxins, which are also electron-transfer proteins. The [3Fe—4S] voided cubane stmcture (11) has been found in some ferredoxins and in the inactive form of aconitase, the enzyme which catalyzes the stereospecific hydration—rehydration of citrate to isocitrate in the Krebs cycle. In addition, enzymes are known that contain either other types of iron sulfur clusters or iron sulfur clusters that include other metals. Examples include nitrogenase, which reduces N2 to NH at a MoFe Sg homocitrate cluster carbon monoxide dehydrogenase, which assembles acetyl-coenzyme A (acetyl-CoA) at a FeNiS site and hydrogenases, which catalyze the reversible reduction of protons to hydrogen gas. 

Fig. 7. View of the FeMo-cofactor prosthetic group of the nitrogenase MoFe protein with some of the surrounding amino acid residues where ( ) represents the molybdenum coordinated to a-His-442 and homocitrate (at the top), ( ) represents the iron, interspersed with the sulfur (O) and carbon...

The MoFe proteins are all a2 2 tetramers of 220-240 kDa, the a and (3 subunits being encoded by the nifD and K genes, respectively. The proteins can be described as dimers of a(3 dimers. They contain two unique metallosulfur clusters the MoFeTSg homocitrate, FeMo-cofactors (FeMoco), and the FesSy, P clusters. Neither of these two types of cluster has been observed elsewhere in biology, nor have they been synthesized chemically. Each molecule of fully active MoFe protein contains two of each type of cluster 2-7). 

FeMoco can be extracted from the MoFe protein into A(-methylfor-mamide (NMF) solution 32) and has been analyzed extensively using a wide range of spectroscopic techniques both bound to the protein and in solution after extraction from it (33). The extracted FeMoco can be combined with the MoFe protein polypeptides, isolated from strains unable to synthesize the cofactor, to generate active protein. The structure of the FeMoco is now agreed 4, 5, 7) as MoFeTSg homocitrate as in Fig. 4. FeMoco is bound to the a subunit through residues Cys 275, to the terminal tetrahedral iron atom, and His 442 to the molybdenum atom (residue numbers refer to A. vinelandii). A number of other residues in its environment are hydrogen bonded to FeMoco and are essential to its activity (see Section V,E,2). The metal... 

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. 

It is clear from these data that homocitrate is intimately involved in the mechanism of substrate reduction and that close homologs such as citrate cannot entirely fill this role. Rationalization of this phenomenon is difficult, but comparisons of the reactivity of extracted FeMoco from the MoFe protein from wild type and NifV strains have led to an intellectually satisfying explanation (see Section V,E,2). 

However, when the X-ray crystal structure of the MoFe protein was examined, it was clear that homocitrate could not directly hydrogen bond to the histidine, since the carboxylate group and imidazole are stacked parallel to each other in the crystal. Nevertheless, as noted in the previous section, studies on model complexes have suggested that homocitrate can become monodentate during nitrogenase turnover, with the molybdenum carboxylate bond breaking to open up a vacant site at molybdenum suitable for binding N2. 

Forming a hydrogen bond between (i )-homocitrate and His 442 could effectively release electron density into the cluster. Studies on structurally defined N2 complexes have shown that the binding of N2 to a metal site and its ability to be protonated are favored by electron-rich sites. Thus, it is postulated that the electron-richness of the... 

G Lihong, M. Madden,VK. Shah, RH. Burris (1990) Citrate substitutes for homocitrate in nitrogenase of a nifV mutant of Klebsiella pneumoniae. Biochemistry, 29 8577-8581... 

An extensive H-bonding network exists in the vicinity of homocitrate and nearby bridging sulfides. 

Homocitrate acting as acid/base catalyst for protonating bound substrates or metal centers to produce hydrides... 

Homocitrate acting as a leaving group modulating the reduction potential of Mo and opening up coordination sites for hydrides... 

These examples would seem to indicate that the molybdenum atom, that for a long time was considered to be the specific site of dinitrogen coordination, is of little importance. It should be borne in mind, however, that the X-ray structure of the protein was obtained in the resting state. As noted, under such conditions, the Mo atom is assigned oxidation state IV and has a saturated coordination, hence not able to further coordinate nitrogen. EXAFS studies on the active protein indicate a Mo coordination different to that determined by X-ray diffraction. One hypothesis considers the dissociation of the homocitrate, induced by addition of electrons, that would leave vacant coordination sites which could then be saturated by the nitrogen molecule. 

GLYCINE ACETYLTRANSFERASE HOMOCITRATE SYNTHASE HOMOSERINE O-ACETYLTRANSFERASE... 

STEREOCHEMICAL TERMINOLOGY, lUPAC RECOMMENDATIONS HOMOCITRATE SYNTHASE Homoconjugation,... 

Fig. 15. Structure of the homocitrate component of the nitrogenase iron-molybdenum cofactor.

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