Nucleotide-binding folds

ABC Transporters. Figure 1 Structure of ABCB 1, ABCC1, and ABCG2 (NBF nucleotide binding fold TMD transmembrane domaine. Modified according to www.iwaki-kk.co.jp/bio/specialedition/se02.htm). 

The breast cancer resistance protein (BCRP) belongs to the G-branch of the ABC-transporter family (ABCG2). In contrast to most other ABC-proteins, BCRP consists of only one transmembrane domain (TDM) with one nucleotide binding fold (NBF) at its C-terminus. Because of this structural characteristic BCRP as well as other ABC-transporters with only one TMD are termed half transporters. To achieve functional activity these transporters have to form hetero- or homodimers. BCRP is involved in the multidrug resistance of certain tumors and transports endogenous compounds like cholesterol and steroid hormones. 

The functions of a large proportion of the proteins encoded by the human genome are presently unknown. Recent advances in bioinformatics permit researchers to compare amino acid sequences to discover clues to potential properties, physiologic roles, and mechanisms of action of proteins. Algorithms exploit the tendency of nature to employ variations of a structural theme to perform similar functions in several proteins (eg, the Rossmarm nucleotide binding fold to bind NAD(P)H,... 

Figure 41-17. Diagram of the structure of the CFTR protein (not to scale). The protein contains twelve transmembrane segments (probably helical), two nucleotide-binding folds or domains (NBFl and NBF2), and one regulatory (R) domain. NBFl and NBF2 probably bind ATP and couple its hydrolysis to transport of Cl . Phe 508, the major locus of mutations in cystic fibrosis, is located in NBFl.

Walker, J. E., Saraste, M., Runswick, M. J. and Gay, N. J. (1982). Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold, EMBO J., 1, 945-951. 

The structure of the isoleucyl-tRNA synthetase (IleRS) from Thermus ther-mophilus (1045 residues, Mr 120 000) has been solved, as well as its complexes with lie and Val.17 The protein contains a nucleotide binding fold (Chapter 1) that binds ATR The fold has two characteristic ATP binding motifs His-54-Val-55-Gly-56-His-57 and Lys-591-Met-592-Ser-593-Lys-594. In the L-Ile-IleRS complex, a single He is bound at the bottom of the ATP cleft, with the hydrophobic side chain in a hydrophobic pocket, surrounded by Pro-46, Trp-518, and Trp-558. L-Leucine cannot fit into this pocket because of the steric hindrance of one of its terminal methyl groups. Larger amino acids are similarly excluded from this site. In the l-Val-IleRS complex, Val is bound to the same site, but the... 

Thomas PM, Wohllk N, Huang E, Kuhnle U, Rabl W, Gagel RF, Cote GJ. Inactivation of the first nucleotide-binding fold of the sulfonylurea receptor, and familial persistent hyperinsulinemic hypoglycemia of infancy. Am J Hum Genet 1996 59(3) 510-518. 

Surface-exposed parts of the protein have been distinguished by their ability to bind specific antibodies and proteolytic enzymes under nondenaturing conditions (see Figure 16). Many of these epitopes are located at positions in the sequence that correspond to the external side of the suggested nucleotide-binding fold (Mate et al., 1992). Antibodies to fluorescein bind only to denatured FITC-labeled Ca2+-ATPase, and not to the native FITC-labeled enzyme. This is consistent with a location of bound FITC in a hydrophobic cleft corresponding to the ATP site. 

K., Matsuo, M., Tucker, S.J., Komano, T, Amachi, T, and Ueda, K. (1998) Nonequivalent cooperation between fhe two nucleotide-binding folds of P-glycoprotein. Biochimica et Biophysica Acta. 1373 (1), 131-136. 

G. Lenoir, S. Blanquet, J. Y. Lallemand. Insight into cystic fibrosis by structural modelling of CFTR first nucleotide binding fold (NBF1). CRAcad Sci III. 1997, 320, 113-121. 

Structural elements forms a fold, such as the nucleotide binding fold, or an actin fold. Folds are defined by their similarity in a number of different proteins. 

Fig. 7.8. Ribbon drawing showing the arrangement of secondary structures into a three-dimensional pattern in domain 1 of lactate dehydrogenase. The individual polyjjeptide strands in the six-stranded P-sheet are shown with arrows. Different strands are connected by helices and by nonrepetitive structures (mrns, coils and loops), shown in blue. This domain is the nucleotide binding fold. NAD is bound to a site created by the helices (upper left of figure.) (Modified from Richardson JS. Adv Protein Chem. The anatomy and taxonomy of protein structure 1981 34 167).

Folds are relatively large patterns of three-dimensional strnctnre that have been recognized in many proteins, including proteins from different branches of the phylogenetic tree. A characteristic activity is associated with each fold, such as ATP binding and hydrolysis (the actin fold) or NAD binding (the nucleotide-binding fold). These three examples of fold patterns are discussed below. 

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