Structure, three-dimensional subunits

Some proteins can be complex, when they contain multiple subunits of polypeptide structural entities. The way in which three-dimensional subunits interact to form the complete functional protein is called the quaternary structure of a protein. This level of hierarchy is possible only if the protein has multiple units. An example is hemoglobin. 

Figure 12.14 The three-dimensional structure of a photosynthetic reaction center of a purple bacterium was the first high-resolution structure to be obtained from a membrane-bound protein. The molecule contains four subunits L, M, H, and a cytochrome. Subunits L and M bind the photosynthetic pigments, and the cytochrome binds four heme groups. The L (yellow) and the M (red) subunits each have five transmembrane a helices A-E. The H subunit (green) has one such transmembrane helix, AH, and the cytochrome (blue) has none. Approximate membrane boundaries are shown. The photosynthetic pigments and the heme groups appear in black. (Adapted from L. Stryer, Biochemistry, 3rd ed. New York ...

When they form the three subunits A, B, and C of the asymmetric unit, the identical polypeptides adopt different three-dimensional structures. The C subunit in particular is distinct from the A and B structures, its hinge region assuming a different conformation so that the S and P domains are... 

Since all members of this family of RNA phages have homologous coat proteins, their subunits are expected to have the same three-dimensional structure. It remains to be seen if the MS2 fold is also present in any other unrelated viruses. The fold is so far unique for the MS2 subunit, but similar structures have been observed in other proteins such as the major histocompatibility antigen, HLA, which was discussed in Chapter 15. 

Despite the unity in secondary structural patterns, little is known about the three-dimensional, or tertiary, structure of rRNAs. Even less is known about the quaternary interactions that occur when ribosomal proteins combine with rRNAs and when the ensuing ribonucleoprotein complexes, the small and large subunits, come together to form the complete ribosome. Furthermore, assignments of functional roles to rRNA molecules are still tentative and approximate. (We return to these topics in Chapter 33.)... 

Figure 3 shows the three-dimensional structure of the MoFe protein from Klebsiella pneumoniae, Kpl, obtained at 1.65-A resolution (7). The overall structure of the polypeptides is frilly consistent with that reported earlier for Avl (3). The a and /8 subunits exhibit similar polypeptide folds with three domains of parallel /3 sheet/a helical type. At the interface between the three domains in the a subunit is a wide shallow cleft with the FeMoco at the bottom of the cleft about 10 A from the solvent. FeMoco is enclosed within the a subunit. The P cluster, however, is buried within the protein at the interface between the a and /8 subunits, being bound by cysteine residues from each subunit. A pseudo-twofold rotation axis passes between the two halves of the P cluster and relates the a and (3 subunits. Each af3 pair of subunits contains one FeMoco and one P cluster and thus appears... 

Fig. 1. Ribbon representation of the three-dimensional structure of D. gigas hydro-genase (32). The large subunit is represented in dark gray. Fe is represented by black spheres, Ni by gray spheres, and inorganic sulfur by white spheres. The C-terminal end of the large subunit is close to the Ni smd completely buried in the structure.

Finally, to produce the structural and functional devices of the cell, polypeptides are synthesized by ribosomal translation of the mRNA. The supramolecular complex of the E. coli ribosome consists of 52 protein and three RNA molecules. The power of programmed molecular recognition is impressively demonstrated by the fact that aU of the individual 55 ribosomal building blocks spontaneously assemble to form the functional supramolecular complex by means of noncovalent interactions. The ribosome contains two subunits, the 308 subunit, with a molecular weight of about 930 kDa, and the 1590-kDa 50S subunit, forming particles of about 25-nm diameter. The resolution of the well-defined three-dimensional structure of the ribosome and the exact topographical constitution of its components are still under active investigation. Nevertheless, the localization of the multiple enzymatic domains, e.g., the peptidyl transferase, are well known, and thus the fundamental functions of the entire supramolecular machine is understood [24]. 

Diamondoids show unique properties due to their exceptional atomic arrangements. Adamantane consists of cyclohexane rings in chair conformation. The name adamantine is derived from the Greek word for diamond since its chemical structure is like the three-dimensional diamond subunit, as shown in Fig. 5. 

Imately 65 X 55 X 50 It Is composed of four polypeptide chains each resembling quite closely the myoglobin chain The three dimensional structure of the subunits Is held together by weak noncovalent bonds The polar amino acid side chains are In contact with the solvent, and the nonpolar residues are located In the Interior of the molecule or In regions which form the contacts between chains The heme group Is located In a pocket In each chain residues In contact with heme are Invariable ( e are the same In different mammalian hemoglobins) and the bonds between heme and chain are hydrophobic Interactions Contacts between like chains (a-a are... 

Glutathione reductase (GR) catalyzes the reduction of oxidized glutathione (GSSG) to reduced glutathione (GSH) using NADPH provided from the hexose monophosphate pathway. GR, a ubiquitous flavoenzyme, maintains a high value of two for the GSH/GSSG ratio in the red blood cells. l,3-Bis(2-chloroethyl)-nitrosourea (BCNU) selectively inhibits cellular GR. GR is composed of two identical subunits, each of molecular mass 50 kDa (S8). The three-dimensional structure and mechanism of catalysis have been established for human GR (K17). 

Normal hemoglobin molecules are complex, three-dimensional structures consisting of four chains of amino acids known as polypeptide chains. Two of these chains are known as alpha subunits with 141 amino acid residues each, and the remaining polypeptide chains are the beta subunits with 146 amino acid residues each. The sequences of amino acids in the alpha and beta subunits are different, but fold up via noncovalent interactions to form similar three-dimensional structures. When a polypeptide chain arranges itself in space, i.e., when it folds, amino acids that were far apart in the chain are brought closer in proximity. The final overall shape of the protein molecule is influenced by (1) the amino acids in the chain, and (2) the interactions that are possible between distant amino acids. 

Gene Subunit Amino acid substitution in polymorphic variants K, [Ethanol] [mM] Turnover rate [min-1] Three- dimensional structure... 

Goldberg, J., Huang, H. B., Kwon,Y. G., Greengard, P., Nairn, A. C. and Kuriyan, J. Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1. Nature 376 745-753,1995. 

IMPases have been purified from bovine brain [91,107] and rat brain [106]. The enzymes from human brain [112] and bovine brain [113] have also been cloned and expressed in and purified from E. coli. The enzyme is functionally active as a homodimer comprising two 30 kDa subunits. The three-dimensional structure of the human IMPase complexed with Gd3+ and sulfate has been determined by X-ray crystallography [114] and was initially analyzed to identify the potential active site. 

---