The TraI protein of conjugative plasmid F factor binds and cleaves a single-stranded region of the plasmid prior to transfer to a recipient. TraI36, an N-terminal TraI fragment, binds ssDNA with a subnanomolar K(D) and remarkable sequence specificity. The structure of the TraI36 Y16F variant bound to ssDNA reveals specificity determinants, including a ssDNA intramolecular 3 base interaction and two pockets within the protein's binding cleft that accommodate bases in a knob-into-hole fashion. Mutagenesis results underscore the intricate design of the binding site, with the greatest effects resulting from substitutions for residues that both contact ssDNA and stabilize protein structure. The active site architecture suggests that the bound divalent cation, which is essential for catalysis, both positions the DNA by liganding two oxygens of the scissile phosphate and increases the partial positive charge on the phosphorus to enhance nucleophilic attack.

We have isolated and sequenced cDNAs for corticosteroid binding globulin (CBG) Corticosteroid binding globulin (CBG) is the major transport protein for glucocorticoids in the blood of almost all vertebrate species (1), and >90% of the cortisol in human plasma is bound by this protein (2). The remaining fraction is distributed more evenly between albumin and the pool of nonprotein-bound or "free" steroid that is generally assumed to be biologically active (2, 3). In humans, CBG is an acidic, -58-kDa glycoprotein (4-6) comprising five N-linked oligosaccharide chains (7) that collectively represent -23% of the molecule by mass (6, 7). The binding site for natural glucocorticoids appears to be a hydrophobic pocket containing one of two cysteine residues that have been identified by amino acid composition analyses (8)(9)(10)(11). Apart from this information, and the identification of eight residues at the NH2 terminus of human CBG (5, 11), there is virtually no information about its primary structure or the location of its steroid binding site.Like many other plasma transport proteins, CBG is produced and secreted by hepatocytes (12), but has also been identified in a number of glucocorticoid responsive cells (2, 13), and may even interact directly with the plasma membranes of some cells (14,15). The objectives of this study were, therefore, to predict the amino acid sequence of human CBG from a cDNA and to determine whether tissues other than the liver possess the capacity to produce this protein. § METHODS cDNA Cloning. A monospecific rabbit antiserum for human CBG (6) was initially used to screen a Xgtll human liver cDNA library that was kindly provided by S. L. C. Woo (Baylor College of Medicine, Houston). The screening method was based on the technique described by Young and Davis (16), with the exception that peroxidase-labeled protein A was used to detect antibody-antigen complexes in the presence of the chromogenic substrate 4-chloro-1-naphthol. The recombinant phage isolated in this way were used to prepare plate lysates using NZC top agar (GIBCO). The phage were harvested and purified, and the cDNA inserts were excised and inserted into the EcoRI site of pBR322 according to Maniatis et al. (17). Plasmids containing CBG cDNAs were used to transform competent Escherichia coli (strain MM 294), and transformants were propagated in Luria broth in the presence of ampicillin and chloramphenicol to amplify the plasmid (17). Plasmids were isolated by the alkaline lysis method and purified using benzoylated-naphthoylated-DEAE cellulose (Sigma) according to Gamper et al. (18). The cDNAs were routinely excised from the plasmid and purified by polyacrylamide gel electrophoresis, prior to nick-translation with 32P-labeled dCTP (17).In an attempt to isolate a full-length CBG cDNA, the radiolabeled cDNA was employed to rescreen the library. Nitrocellulose filters (Schleicher & Schuell; BA85, 0.45-,um pore size) were used to transfer DNA and were hybridized with 2 x 106 dpm of the CBG cDNA probe per ml, in the pr...

We have sequenced a cDNA for sex hormone-binding globulin (SHBG) isolated from a phage 2gtl 1 human liver cDNA library. The library was screened with a radiolabeled rat androgen-binding protein (ABP) cDNA, and the abundance of SHBG cDNAs was 1 in 750 000 plaques examined. The largest human SHBG cDNA (1194 base-pairs) contained a reading frame for 381 amino acids. This comprised 8 amino acids of a signal peptide followed by 373 residues starting with the known NH2-terminal sequence of human SHBG, and ending with a termination codon. The predicted polypeptide Mr of SHBG is 40 509, and sites of attachment of one O-linked (residue 7) and two N-linked oligosaccharide (residues 351 and 367) chains were identified. Purified SHBG was photoaffinity-labeled with zt6-[3H]testosterone and cleaved with trypsin. The labeled tryptic fragment was isolated by reverse-phase HPLC, and its NH2-terminal sequence was determined. The results suggest that a portion of the steroid-binding domain of SHBG is located between residue 296 and the 35 predominantly hydrophilic residues at the C-terminus of the protein.cDNA cloning; Amino acid sequence; Sex hormone-binding globulin; Steroid-binding domain

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Bacterial conjugation, transfer of a single strand of a conjugative plasmid between bacteria, requires sequence-specific single-stranded DNA endonucleases called relaxases or nickases. Relaxases contain an HUH (His-hydrophobe-His) motif, part of a three-His cluster that binds a divalent cation required for the cleavage reaction. Crystal structures of the F plasmid TraI relaxase domain, with and without bound single-stranded DNA, revealed an extensive network of interactions involving HUH and other residues. Here we study the roles of these residues in TraI function. Whereas substitutions for the three His residues alter metal-binding properties of the protein, the same substitution at each position elicits different effects, indicating that the residues contribute asymmetrically to metal binding. Substitutions for a conserved Asp that interacts with one HUH His demonstrate that the Asp modulates metal affinity despite its distance from the metal. The bound metal enhances binding of ssDNA to the protein, consistent with a role for the metal in positioning the scissile phosphate for cleavage. Most substitutions tested caused significantly reduced in vitro cleavage activities and in vivo transfer efficiencies. In summary, the results suggest that the metal-binding His cluster in TraI is a finely tuned structure that achieves a sufficient affinity for metal while avoiding the unfavorable electrostatics that would result from placing an acidic residue near the scissile phosphate of the bound ssDNA.Bacterial conjugation contributes to diversification of prokaryotic genomes through horizontal transfer of conjugative plasmids between bacteria. During conjugation, a single strand of the plasmid is cleaved in the donor cell and transferred to the recipient bacterium using plasmid-encoded secretion machinery (1). Conjugation may play important roles in evolution of pathogenic Escherichia coli (2) and the formation of biofilms (3). Despite its importance in genetic diversification and the acquisition of new traits, however, the mechanism of bacterial conjugation is still a relatively poorly understood process.Initiation of conjugation requires strand-and site-specific cleavage of the plasmid within the origin of transfer (oriT) at a site termed nic. The relaxase or mobilization (Mob) protein encoded by the plasmid carries out the metal-dependent cleavage reaction. TraI is the relaxase for F plasmid (4, 5). The cleavage reaction is facilitated by accessory proteins that recruit TraI to oriT, perhaps by directly interacting with the relaxase or creating a favorable DNA conformation for the relaxase to bind (6 -8). The cleavage reaction results in a long-lived physical link between the plasmid and the relaxase, through a phosphotyrosyl bond bridging the catalytic tyrosine residue and the DNA backbone (9, 10). After transfer of the plasmid to the recipient, possibly as a protein-DNA conjugate (11), the cut plasmid is recircularized, most likely by the relaxase, and second strand synthesis occurs. The process produces a donor an...