Howard Zalkin

Enzymes Utilizing Glutamine as an Amide Donor

Amide nitrogen from glutamine is a major source of nitrogen atoms incorporated biosynthetically into other amino acids, purine and pyrimidine bases, amino-sugars, and coenzymes. A family comprised of at least sixteen amidotransferases are known to catalyze amide nitrogen transfer from glutamine to their acceptor substrates. Recent fine structural advances, largely as a result of X-ray crystallography, now provide structure-based mechanisms that help to explain fundamental aspects of the catalytic and regulatory interactions of several of these aminotransferases. This chapter provides an overview of this recent progress made on the characterization of amidotransferase structure and mechanism.

Mechanism of corepressor-mediated specific DNA binding by the purine repressor.

The modulation of the affinity of DNA-binding proteins by small molecule effectors for cognate DNA sites is common to both prokaryotes and eukaryotes. However, the mechanisms by which effector binding to one domain affects DNA binding by a distal domain are poorly understood structurally. In initial studies to provide insight into the mechanism of effector-modulated DNA binding of the lactose repressor family, we determined the crystal structure of the purine repressor bound to a corepressor and purF operator. To extend our understanding, we have determined the structure of the corepressor-free corepressor-binding domain of the purine repressor at 2.2 A resolution. In the unliganded state, structural changes in the corepressor-binding pocket cause each subunit to rotate open by as much as 23 degrees, the consequences of which are the disengagement of the minor groove-binding hinge helices and repressor-DNA dissociation.

The X-ray Structure of the PurR-Guanine-purF Operator Complex Reveals the Contributions of Complementary Electrostatic Surfaces and a Water-mediated Hydrogen Bond to Corepressor Specificity and Binding Affinity

The purine repressor, PurR, is the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric transcription factor is activated to bind to cognate DNA operator sites by initially binding either of its physiologically relevant, high affinity corepressors, hypoxanthine (K d = 9.3 μm) or guanine (K d = 1.5 μm). Here, we report the 2.5-Å crystal structure of the PurR-guanine-purF operator ternary complex and complete the atomic description of 6-oxopurine-induced repression by PurR. As anticipated, the structure of the PurR-guanine-purFoperator complex is isomorphous to the PurR-hypoxanthine-purF operator complex, and their protein-DNA and protein-corepressor interactions are nearly identical. The former finding confirms the use of an identical allosteric DNA-binding mechanism whereby corepressor binding 40 Å from the DNA-binding domain juxtaposes the hinge regions of each monomer, thus favoring the formation and insertion of the critical minor groove-binding hinge helices. Strikingly, the higher binding affinity of guanine for PurR and the ability of PurR to discriminate against 2-oxopurines do not result from direct protein-ligand interactions, but rather from a water-mediated contact with the exocyclic N-2 of guanine, which dictates the presence of a donor group on the corepressor, and the better electrostatic complementarity of the guanine base and the corepressor-binding pocket.

De novo purine nucleotide biosynthesis: cloning, sequencing and expression of a chicken PurH cDNA encoding 5-aminoimidazole-4-carboxamide-ribonucleotide transformylase-IMP cyclohydrolase

The purH cDNA, encoding 5-aminoimidazole-4-carboxamide-ribonucleotide (AICAR) transformylase-inosine monophosphate cyclohydrolase (ATIC), was cloned by functional complementation of an Escherichia coli purH mutant using a chicken liver cDNA expression library. This represents the first report of the cloning of any eukaryotic ATIC-encoding cDNA (PurH). The avian ATIC mRNA is 2.3 kb long and encodes a protein with an Mr of 64,422. The deduced amino acid sequence is 36% identical to the bacterial purH-encoded enzymes from Bacillus subtilis and E. coli. The avian cDNA was expressed as a glutathione S-transferase (GST) fusion protein that was purified in a single step by affinity chromatography. A novel vector was employed which permits rapid and highly efficient cleavage of the GST fusion protein yielding 10 mg of purified PurH product per liter of bacterial culture. Km values were determined with the purified fusion protein utilizing AICAR and (6-R)N10-formyl-tetrahydrofolate as substrates. These values compare favorably with the isolated avian enzyme, supporting the idea that kinetic, as well as other physical properties of the recombinant fusion protein are similar to the native avian enzyme. Large quantities of purified enzyme and the ability to generate site-directed mutations should make mechanistic studies possible. The recombinant enzyme also affords a simple and reliable approach to identifying new antifolates.

Coexpression of two closely linked avian genes for purine nucleotide synthesis from a bidirectional promoter.

Two avian genes encoding essential steps in the purine nucleotide biosynthetic pathway are transcribed divergently from a bidirectional promoter element. The bidirectional promoter, embedded in a CpG island, directs coexpression of GPAT and AIRC genes from distinct transcriptional start sites 229 bp apart. The bidirectional promoter can be divided in half, with each half retaining partial activity towards the cognate gene. GPAT and AIRC genes encode the enzymes that catalyze step 1 and steps 6 plus 7, respectively, in the de novo purine biosynthetic pathway. This is the first report of genes coding for structurally unrelated enzymes of the same pathway that are tightly linked and transcribed divergently from a bidirectional promoter. This arrangement has the potential to provide for regulated coexpression comparable to that in a prokaryotic operon.

Tyrosine-inhibited 3-deoxy-d-arabino-heptulosonate 7-phosphate synthetase: Properties of the partially purified enzyme from Salmonella typhimurium

Abstract Tyrosine-regulated 3-deoxy- d - arabino -heptulosonate 7-phosphate (DAHP) synthetase has been partially purified from Salmonella typhimurium . Properties of the enzyme and aspects of the reaction mechanism were studied. Lineweaver-Burk plots for saturation by phosphoenolpyruvate and erythrose 4-P yield families of parallel or nearly parallel lines suggesting the possibility of a ping-pong mechanism. A sequential mechanism is, however, not excluded. Stabilization of the enzyme to heat inactivation by phosphoenolpyruvate suggests that erythrose 4-P is not required for binding of phosphoenolpyruvate. The DAHP synthetase reaction was studied in ( 18 O)H 2 O. P i , formed concomitantly with synthesis of DAHP, does not contain 18 O. This requires splitting of the CO bond of phosphoenolpyruvate and indicates direct elimination of phosphate. These results suggest that the enzyme reacts with phosphoenolpyruvate to form an uncharacterized enzyme-substrate intermediate and P i . Reaction of erythrose 4-P with the enzyme-substrate intermediate could yield the product DAHP and enzyme. Feedback inhibition of the enzyme by tyrosine is dependent upon pH. The Hill coefficient, n ′, is 1.4 at both pH 6.0 (85% inhibition by 0.1 m m tyrosine) and at pH 8.0 (25% inhibition by 0.1 m m tyrosine), thus suggesting cooperative interaction of tyrosine sites. Treatment of the enzyme with p -mercuribenzoate causes activation at concentrations lower than 1 μ m and inhibition at higher concentrations but does not affect inhibition by tyrosine. Enzymatic activity is dependent on Co 2+ .

The Purine Repressor of Bacillus subtilis: a Novel Combination of Domains Adapted for Transcription Regulation

The purine repressor from Bacillus subtilis, PurR, represses transcription from a number of genes with functions in the synthesis, transport, and metabolism of purines. The 2.2-A crystal structure of PurR reveals a two-domain protein organized as a dimer. The larger C-terminal domain belongs to the PRT structural family, in accord with a sequence motif for binding the inducer phosphoribosylpyrophosphate (PRPP). The PRT domain is fused to a smaller N-terminal domain that belongs to the winged-helix family of DNA binding proteins. A positively charged surface on the winged-helix domain likely binds specific DNA sequences in the recognition site. A second positively charged surface surrounds the PRPP site at the opposite end of the PurR dimer. Conserved amino acids in the sequences of PurR homologs in 21 gram-positive bacteria cluster on the proposed recognition surface of the winged-helix domain and around the PRPP binding site at the opposite end of the molecule, supporting a common function of DNA and PRPP binding for all of the proteins. The structure supports a binding mechanism in which extended regions of DNA interact with extensive protein surface. Unlike most PRT proteins, which are phosphoribosyltransferases (PRTases), PurR lacks catalytic activity. This is explained by a tyrosine side chain that blocks the site for a nucleophile cosubstrate in PRTases. Thus, B. subtilis has adapted an enzyme fold to serve as an effector-binding domain and has used it in a novel combination with the DNA-binding winged-helix domain as a repressor of purine genes.

Interdomain Signaling in Glutamine Phosphoribosylpyrophosphate Amidotransferase

The glutamine phosphoribosylpyrophosphate (PRPP) amidotransferase-catalyzed synthesis of phosphoribosylamine from PRPP and glutamine is the sum of two half-reactions at separated catalytic sites in different domains. Binding of PRPP to a C-terminal phosphoribosyltransferase domain is required to activate the reaction at the N-terminal glutaminase domain. Interdomain signaling was monitored by intrinsic tryptophan fluorescence and by measurements of glutamine binding and glutamine site catalysis. Enzymes were engineered to contain a single tryptophan fluorescence reporter in key positions in the glutaminase domain. Trp83 in the glutamine loop (residues 73–84) and Trp482 in the C-terminal helix (residues 471–492) reported fluorescence changes in the glutaminase domain upon binding of PRPP and glutamine. The fluorescence changes were perturbed by Ile335 and Tyr74 mutations that disrupt interdomain signaling. Fluoresence titrations of PRPP and glutamine binding indicated that signaling defects increased theK d for glutamine but had little or no effect on PRPP binding. It was concluded that the contact between Ile335 in the phosphoribosyltransferase domain and Tyr74 in the glutamine site is a primary molecular interaction for interdomain signaling. Analysis of enzymes with mutations in the glutaminase domain C-terminal helix and a 404–420 peptide point to additional signaling interactions that activate the glutamine site when PRPP binds.

Utilization of ammonia for tryptophan synthesis

Abstract A strain of Escherichia coli in which the glutamine amidotransferase function (anthranilate synthetase component II) of anthranilate synthetase has been deleted synthesizes tryptophan using NH3-dependent anthranilate synthetase component I (AS-I). In NH3-limited media this strain is a tryptophan auxotroph. Mutants that acquired the capacity to grow in NH3-limited media were isolated. Growth of mutant strains in NH3-limited media correlates with increased AS-I activity. Glutamine-dependent AS activity was not found in any of the mutant strains indicating that another glutamine amidotransferase had not been recruited to function with AS-I.

Mutations in the Bacillus subtilis purine repressor that perturb PRPP effector function in vitro and in vivo.

The Bacillus subtilis pur operon repressor (PurR) has a PRPP (5-phosphoribosyl 1-pyrophosphate) binding motif at residues 199–211. Two PurR PRPP binding region mutations (D203A and D204A) were constructed, and the effects on binding of repressor to the pur operon control site in vitro and on regulation of pur operon expression in vivo were investigated. PRPP significantly inhibited the binding of wild-type but not mutant PurR to pur operon control site DNA. In strains with the D203A and D204A mutations, pur operon expression in vivo was super-repressed by addition of adenine to the growth medium. These results support the role of PRPP in modulating the regulatory function of PurR in vivo. YabJ, the product of the distal gene in the bicistronic purR operon, is also required for PurR function in vivo.