Homodimeric proteins

Finally, also isolated from D. vulgaris was another homodimeric protein (subunit molecular mass of 27 kDa) named nigerythrin (43). Spectroscopic characterization revealed that this protein is similar to Rr. The function of nigerythrin is also unknown. It should be noted that genes coding for two similar Rr proteins were also found in Arch-aeoglobus fulgidus. 

TKase is a homodimeric protein with a subunit of about 70kDa. The X-ray structures of TKase of E. colif S. cerevisiaeX Leishmania mexicana and mize have been solved. In addition, the crystal structures of a number of site-directed mutants have been determined. Schneider and co-workers have reported a series of studies in which they have mutated important residues of active site of TKase to elucidate the reaction mechanism and explain the origin of the stereospecificity of the C—C bond-forming process (Table The conserved... 

Rbo is a homodimeric protein, each subunit of which contains two distinct mononuclear nonheme iron centers in separate domains (Fig. 10.4) (Coehlo et al. 1997). Center I contains a distorted rubredoxin-type [Fe(SCys)4] coordination sphere. [Fe(SCys)4] sites in proteins are known to catalyze exclusively electron transfer, which is, therefore, the putative function for center I. Center II contains a unique [Fe(NHis)4(SCys)] site that is rapidly oxidized by 0, and is, therefore, the likely site of superoxide reduction (Lombard et al. 2000). A blue nonheme iron protein, neelaredoxin (Nlr) from Desulfovibrio gigas (Silva et al. 1999), contains an iron center closely resembling that of Rbo center II (Table 10.1). The blue color is due to the oxidized (i.e., Fe(III)) form [Fe(NHis)4(SCys)] site, which, in both Nlr and Rbo, has a prominent absorption feature at -650 nm. Reduction of center II to its Fe(II) form fully bleaches its visible absorption. These absorption features have been used to probe the reactivity of Rbo with superoxidie. 

A second group of ribonucleotide reductases (Class II), found in many bacteria, depend upon the cobalt-containing vitamin B12 coenzyme which is discussed in Section B. These enzymes are monomeric or homodimeric proteins of about the size of the larger a subunits of the Class I enzymes. The radical generating center is the 5 -deoxyadenosyl coenzyme.350 364 365... 

Figure 16-31 (A) Structure of molybdopterin cytosine dinucleotide complexed with an atom of molybdenum. (B) Stereoscopic ribbon drawing of the structure of one subunit of the xanthine oxidase-related aldehyde oxidoreductase from Desulfo-vibrio gigas. Each 907-residue subunit of the homodimeric protein contains two Fe2S2 clusters visible at the top and the molybdenum-molybdopterin coenzyme buried in the center. (C) Alpha-carbon plot of portions of the protein surrounding the molybdenum-molybdopterin cytosine dinucleotide and (at the top) the two plant-ferredoxin-like Fe2S2 clusters. Each of these is held by a separate structural domain of the protein. Two additional domains bind the molybdopterin coenzyme and there is also an intermediate connecting domain. In xanthine oxidase the latter presumably has the FAD binding site which is lacking in the D. gigas enzyme. From Romao et al.633 Courtesy of R. Huber.

The polyketide synthases responsible for chain extension of cinnamoyl-CoA starter units leading to flavonoids and stilbenes, and of anthraniloyl-CoA leading to quinoline and acridine alkaloids (see page 377) do not fall into either of the above categories and have now been termed Type TTT PKSs. These enzymes differ from the other examples in that they are homodimeric proteins, they utilize coenzyme A esters rather than acyl carrier proteins, and they employ a single active site to perform a series of decarboxylation, condensation, cyclization, and aromatization reactions. 

This reaction is accomplished by several types of iron ribonucleoside reductase (RNR) [1,5,7,13,118], One of the best-characterized RNRs (from E. coli) contains two homodimeric protein components, R1 and R2. The R2 protein comprises an oxygen bridged dinuclear Fe(III) in its oxidized form [119], All RNRs promote the formation of a stable organic radical, which, eventually, leads to the abstraction of a hydrogen atom from the ribose. In the case of E. coli RNR, the latter is accomplished by the R1 protein, specifically by a cysteinyl residue a redox active cystine, also part of Rl, provides the required reducing equivalents (Figure 25). 

Originally isolated and characterized from the petals of Clarkia breweri, salicylic acid carboxyl methyltransferase (SAMT), converts salicylic acid to methylsalicylate.14 Methysalicylate, a volatile ester, has a characteristic wintergreen scent Apart from its putative role in defense, methylsalicylate is an important chemoattractant for moth-pollinated flowers and one of the main volatiles released from Clarkia breweri flowers.44,55 SAMT is a member of the type 3 family of plant MTs. Similarly to the previously discussed families of methyltransferases, type 3 MTs are homodimeric proteins. 

Prostaglandin (PG) H Synthase. The enzyme PGH synthase is a homodimeric protein consisting of subunits with an approximate molecular weight of 72 kDa and one Fe(III)-protoporphyrin IX (PPIXFe(III)) prosthetic group per subunit. This protein is responsible for the central reaction in the biosynthesis of prostaglandins and is selectively inhibited by antiinflammatory drugs such as aspirin and indo-... 

Walsh, S. T., Jevitts, L. M., Sylvester, J. E., and Kossiakoff, A. A. (2003). Site2 binding energetics of the regulatory step of growth hormone-induced receptor homodimerization. Protein Sci. 12(9), 1960-1970. 

This intriguing nonheme homodimeric protein see Iron Proteins with Dinuclear Active Sites), originally isolated from the anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris, contains a unique combination of two types of chromophoric iron(III) sites in each subunit one rubredoxinlike Fe(S-Cys)4 center in the C-terminal domain and one... 

Bahadur, R.P., Chakrabarti, P., Rodier, F. and Janin, J. (2003) Dissecting subunit interfaces in homodimeric proteins. Proteins 53, 708-719. 

Lantibiotics are secreted out of the cell by the LanT ATP-binding cassette transporters. These enzymes are transmembrane, homodimeric proteins that use the energy of ATP hydrolysis to secrete either the mature lantibiotic or a fully modified precursor peptide with the leader sequence still attached. A second type of LanT transporter is found in the... 

V-shaped protein encloses a "chamber within the bilayer where it is hypothesized that bound substrates are flipped across the membrane, as depicted in Figure 7-12. Each identical subunit in this homodimeric protein has one transmembrane domain, comprising six a. helices, and one cytosolic domain where ATP binding occurs. [Adapted from G. Chang and C. Roth, 2001, Science 293 1793.]... 

A FIGURE 11-42 Consensus sequences of DNA response elements that bind three nuclear receptors. The response elements for the glucocorticoid receptor (GRE) and estrogen receptor (ERE) contain inverted repeats that bind these homodimeric proteins. The response elements for heterodimeric receptors contain a common direct repeat separated by three to five base pairs, for the vitamin D3 receptor (VDRE), thyroid hormone receptor (TRE), and retinoic acid receptor (RARE). The repeat sequences are indicated by red arrows. [See K. Umesono etal., 1991, Ce//65 1255, and A. M. Naaretal., 1991, Ce//65 1267]... 

A number of isoenzymes that are related to GST p have since been identified. A hepatic enzyme, called GST ip, has been purified in several laboratories (H27, S26), and it has been shown that this homodimeric protein has an N-terminal amino acid sequence identical to that of GST p (All, HI 6). The expression of this additional mu-class form in human liver is also subject to variation (H63). GST p and GST op are homodimers and it is now generally accepted that these two enzymes represent allelic variants encoded at the GST 1 locus identified by Board (B30) and Strange et al. (S41). Less information is available on the heterodimeric enzyme formed by the combination of p-type and ip-type subunits (H16, V4). The existence of this isoenzyme has been demonstrated by means of starch-gel electrophoresis and chromatofocusing (F2, S41) however, so far, it has not been fully characterized. A third hepatic mu-class enzyme, named GST < ), was identified by Stockman and Hayes (S36). This isoenzyme, which was present in only 1 of 20 livers examined, was shown to be immunologically related to GST p and GST ip but could be distinguished from these forms by its lower isoelectric point and the fact that, unlike GST p and GST ip, it has a blocked N terminus (P. 

The enzyme is a homodimeric protein of A/r 170,000 and contains no known organic or metal ion cofactors. The enzyme is readily inactivated by oxygen and interconverts between active and inactive forms in vivo (173, 174). The activation process occurs under conditions of anaerobiosis and is catalyzed by an Fe(ll)-dependent activating enzyme (Mr 30,000) (775). Elegant studies on the in vitro activation of PFL by Knappe and co-workers (176, 177) have revealed that a complex activation cocktail is required, which includes the activating enzyme, pyruvate, or oxamate as allosteric effectors, S-adenosylmethionine (SAM), and flavodoxin (775) or photoreduced 5-deazariboflavin (178). A possible role for a B12 derivative in the activation or catalytic reaction for PFL is not likely in light of the observation that E. coli 113-3, a methionine/B auxotroph, pos-... 

X-ray crystal structures of CODH/ACS proteins show that they are large (300 kDa) homodimeric proteins with the two CODH domains j3 subunits) at the core, and the two ACS domains (a subunits) tethered to the side of each of these (3 subunits. The (3 subunits each contain one Ni and 10 Fe ions that are arranged into three FeS clusters (the so-called B-, C-, and D-clusters), whereas the a subunits each contains the active site A-cluster, a [Fe4S4] " cubane that is bridged by the sulfur of a cysteinyl residue to the proximal metal (Mp) of a binuclear center. This binuclear center contains a square planar nickel ion, referred to as the distal Ni (Ni(j), which is coordinated by the two thiolates and two backbone amides of a Cys-Gly-Cys motif There has been some debate as to the identity of Mp, as Ni, Cu, and Zn ions have been shown to occupy this site however, it is now generally accepted that the A-cluster is a binuclear Ni—Ni center bridged by a cysteine thiol to a [4Fe— 4S] cluster. " ... 

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