The role of histidine 632 in catalysis by human topoisomerase I

Based on the crystal structure of human topoisomerase I, we hypothesized that hydrogen bonding between the side chain of the highly conserved His(632) and one of the nonbridging oxygens of the scissile phosphate contributes to catalysis by stabilizing the transition state. This hypothesis has been tested by examining the effects of changing His(632) to glutamine, asparagine, alanine, and tryptophan. The change to glutamine reduced both the relaxation activity and single-turnover cleavage activity by approximately 100-fold, whereas the same change at three other conserved histidines (positions 222, 367, and 406) had no significant effect on the relaxation activity. The properties of the mutant protein containing asparagine instead of histidine at position 632 were similar to those of the glutamine mutant, whereas mutations to alanine or tryptophan reduced the activity by approximately 4 orders of magnitude. The reduction in activity for the mutants was not due to alterations in substrate binding affinities or changes in the cleavage specificities of the proteins. The above results for the glutamine mutation in conjunction with the similar effects of pH on the wild type and the H632Q mutant enzyme rule out the possibility that His(632) acts as a general acid to protonate the leaving 5'-oxygen during the cleavage reaction. Taken together, these data strongly support the hypothesis that the only role for His(632) is to stabilize the pentavalent transition state through hydrogen bonding to one of the nonbridging oxygens.     

The human topoisomerase I damage response plays a role in apoptosis

Previous studies have shown that human topoisomerase I cleavage complexes form as a response to various DNA damages in vivo, the so called human topoisomerase I "damage response". It was suggested that this damage response may play a role in DNA repair as well as in apoptosis, but only very few investigations have been done and the significance of the damage response still remains unclear. Here we demonstrate that human topoisomerase I cleavage complexes induced by high doses of UV irradiation are highly stable for up to 48 h. Furthermore, we show that human topoisomerase I cleavage complexes correlate with apoptosis. However, at low UV doses the cleavage complex level was very low and the complexes were repaired. Surprisingly, we found that high levels of stable cleavage complexes were not only found in UV-irradiated cells but also in untreated cells that underwent apoptosis. A possible role of human topoisomerase I in apoptosis is discussed.     

Reconstitution of enzymatic activity by the association of the cap and catalytic domains of human topoisomerase I

When human topoisomerase I binds DNA, two opposing lobes in the enzyme, the cap region (amino acid, residues 175-433) and the catalytic domain (Deltacap, residues 433 to the COOH terminus) clamp tightly around the DNA helix to form the precleavage complex. Although Deltacap contains all of the residues known to be important for catalysis and binds DNA with an affinity similar to that of the intact enzyme, this fragment lacks catalytic activity. However, a mixture of Deltacap and topo31 (residues 175-433) reconstitutes enzymatic activity as measured by plasmid DNA relaxation and suicide cleavage assays. Although the formation of an active complex between topo31 and Deltacap is too unstable to be detected by pull-down experiments even in the presence of DNA, the association of topo31 with Deltacap persists and is detectable after the complex catalyzes the covalent attachment of the DNA to Deltacap by suicide cleavage. Removal of topo31 from Deltacap-DNA after suicide cleavage reveals that, unlike the cleavage reaction, religation does not require the cap region of the protein. These results suggest that activation of the catalytic domain of the enzyme for cleavage requires both DNA binding and the presence of the cap region of the protein.     

Residues within the N-terminal domain of human topoisomerase I play a direct role in relaxation

All eukaryotic forms of DNA topoisomerase I contain an extensive and highly charged N-terminal domain. This domain contains several nuclear localization sequences and is essential for in vivo function of the enzyme. However, so far no direct function of the N-terminal domain in the in vitro topoisomerase I reaction has been reported. In this study we have compared the in vitro activities of a truncated form of human topoisomerase I lacking amino acids 1-206 (p67) with the full-length enzyme (p91). Using these enzyme forms, we have identified for the first time a direct role of residues within the N-terminal domain in modulating topoisomerase I catalysis, as revealed by significant differences between p67 and p91 in DNA binding, cleavage, strand rotation, and ligation. A comparison with previously published studies showing no effect of deleting the first 174 or 190 amino acids of topoisomerase I (Stewart, L., Ireton, G. C., and Champoux, J. J. (1999) J. Biol. Chem. 274, 32950-32960; Bronstein, I. B., Wynne-Jones, A., Sukhanova, A., Fleury, F., Ianoul, A., Holden, J. A., Alix, A. J., Dodson, G. G., Jardillier, J. C., Nabiev, I., and Wilkinson, A. J. (1999) Anticancer Res. 19, 317-327) suggests a pivotal role of amino acids 191-206 in catalysis. Taken together the presented data indicate that at least part(s) of the N-terminal domain regulate(s) enzyme/DNA dynamics during relaxation most probably by controlling non-covalent DNA binding downstream of the cleavage site either directly or by coordinating DNA contacts by other parts of the enzyme.     

The role of topoisomerase I inhibitor in cisplatin-resistant ovarian cancer.

We discussed the role of DNA topoisomerase I (topo I) inhibitor, which is now widely used in clinical practice, in cisplatin-resistant ovarian cancer. Our study showed the synergistic actions between cisplatin and 7-ethyl-10-hydroxycamptothecin (SN-38), an active metabolite of 7-ethyl-10-[4-(1-pyperidino)-1-piperidino]carbonyloxycamptothecin (CPT-11), in two cisplatin-resistant cancer cell lines, HeLa/CDDP and KFr cells, but not in each parent cell line, HeLa and KF cells. Furthermore, HeLa/CDDP cells had a collateral sensitivity to SN-38. The levels of topo I protein in the cisplatin-resistant cells did not differ from those of their parent cell lines and were unaffected by exposure to cisplatin. In contrast, topo I enzymatic activity was 2-4 fold higher in the cisplatin-resistant cell lines compared with their respective parent cell lines. A significant correlation between the sensitivity for SN-38 and topo I activity human clear cell carcinoma cell lines, which are known as intrinsically ciasplatin-resistant cancer, was observed. Next, we examined the relationship between topo I activity and sensitivity to second-line chemotherapy consisting of cisplatin and CPT-11. A total of 30 patients with ovarian cancer who had initially undergone chemotherapy consisting of cisplatin, doxorubicin, and cyclophosphamide (CAP) and exhibited measurable lesions were entered in the study. Tumor samples were obtained in the period between the initial and the second-line chemotherapy. Of those 30 patients, 18 responded to second-line chemotherapy and 12 did not. Topo I activity in tumor samples of responder was significantly greater than that of in nonresponders. In 8 cases whose samples could be obtained before and after CAP, topo I activity significantly increased after CAP therapy. Consequently, the combination therapy with cisplatin and CPT-11 may be effective for patients with cisplatin-resistant ovarian cancer. In addition, topo I enzymatic activity may be a predictor of the sensitivity for topo I inhibitor.     

The role of checkpoint kinase 1 in sensitivity to topoisomerase I poisons

Agents that target topoisomerase I are widely utilized to treat human cancer. Previous studies have indicated that both the ataxia telangiectasia mutated (ATM)/checkpoint kinase (Chk) 2 and ATM- and Rad 3-related (ATR)/Chk1 checkpoint pathways are activated after treatment with these agents. The relative contributions of these two pathways to survival of cells after treatment with topoisomerase I poisons are currently unknown. To address this issue, we assessed the roles of ATR, Chk1, ATM, and Chk2 in cells treated with the topoisomerase I poisons camptothecin and 7-ethyl-10-hydroxycamptothecin (SN-38), the active metabolite of irinotecan. Colony forming assays demonstrated that down-regulation of ATR or Chk1 sensitized cells to SN-38 and camptothecin. In contrast, ATM and Chk2 had minimal effect of sensitivity to SN-38 or camptothecin. Additional experiments demonstrated that the Hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin, which down-regulates Chk1, also sensitized a variety of human carcinoma cell lines to SN-38. Collectively, these results show that the ATR/Chk1 pathway plays a predominant role in the response to topoisomerase I inhibitors in carcinoma cells and identify a potential approach for enhancing the efficacy of these drugs.     

DNA topoisomerase I from human placenta

In this study we report that human placenta is an excellent source of DNA topoisomerase I. The enzyme can be isolated in the fully intact 100 kDa form although lower molecular mass species are also observed. Occasionally, the enzyme can be resolved into two peaks of activity by chromatography on phosphocellulose. As expected, the enzyme promotes marked cleavage of DNA in response to the anticancer drug camptothecin. Because of this property and the ready availability of human placenta, the enzyme should prove to be useful in the development and testing of new anticancer drugs that target topoisomerase I.     

Crucial role of the high-loop lysine for the catalytic activity of arginyl-tRNA synthetase

The presence of two short signature sequence motifs (His-Ile-Gly-His (HIGH) and Lys-Met-Ser-Lys (KMSK)) is a characteristic of the class I aminoacyl-tRNA synthetases. These motifs constitute a portion of the catalytic site in three dimensions and play an important role in catalysis. In particular, the second lysine of the KMSK motif (K2) is the crucial catalytic residue for stabilization of the transition state of the amino acid activation reaction (aminoacyl-adenylate formation). Arginyl-tRNA synthetase (ArgRS) is unique among all of the class I enyzmes, as the majority of ArgRS species lack canonical KMSK sequences. Thus, the mechanism by which this group of ArgRSs achieves the catalytic reaction is not well understood. Using three-dimensional modeling in combination with sequence analysis and site-directed mutagenesis, we found a conserved lysine in the KMSK-lacking ArgRSs upstream of the HIGH sequence motif, which is likely to be a functional counterpart of the canonical class I K2 lysine. The results suggest a plausible partition of the ArgRSs into two major groups, on the basis of the conservation of the HIGH lysine.     

Ionization state and molecular docking studies for the macrophage migration inhibitory factor: the role of lysine 32 in the catalytic mechanism

The macrophage migration inhibitory factor (MIF) is a cytokine that is structurally similar to certain isomerases and for which multiple immune and catalytic roles have been proposed. Different catalytic activities have been reported for MIF, yet the exact mechanism by which MIF acts is not completely known. As a tautomerase, the enzyme uses a general acid-base mechanism of proton transfer in which the amino-terminal proline has been shown to function as the catalytic base. We report the results of molecular docking simulations of macrophage migration inhibitory factor with three substrates, D-dopachrome, L-dopachrome methyl ester and p-(hydroxyphenyl)pyruvate. Electrostatic pK(a) predictions were also performed for the free and complexed forms of the enzyme. The predicted binding mode of p-(hydroxyphenyl)pyruvate is in agreement with the recently published X-ray structure. A model for the binding mode of D-dopachrome and L-dopachrome methyl ester to MIF is proposed which offers insights into the catalytic mechanism of D-dopachrome tautomerase activity of MIF. The proposed catalytic mechanism is further supported by the pK(a) predictions, which suggest that residue Lys32 acts as the general acid for the enzymatic catalysis of D-dopachrome.     

Structure of the human type I DNA topoisomerase gene

We describe the molecular organization of the human gene coding for type I DNA topoisomerase. The coding sequence is split into 21 exons distributed over at least 85 kilobase pairs (kb) of human genomic DNA. The sizes of the 20 introns vary widely between 0.2 and at least 30 kb and all contain the sequence elements known to be required for pre-mRNA splicing. Several of the intron sequences separate exons encoding parts of the enzyme that are highly conserved between human and yeast suggesting that at least some of the exons may code for individual, structurally, or functionally important domains of the enzyme. We also describe the promoter sequence of the human topoisomerase I gene and show that it is composed of distinct functional elements.     

Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant

The functional and structural-dynamical properties of the Lys681Ala mutation in the human topoisomerase IB linker domain have been investigated by catalytic assays and molecular dynamics simulation. The mutant is characterized by a comparable cleavage and a strongly reduced religation rate when compared to the wild type protein. The mutant also displays perturbed linker dynamics, as shown by analysis of the principal components of the motion, and a reduced electrostatic interaction with DNA. Inspection of the inter atomic distances in proximity of the active site shows that in the mutant the distance between the amino group of Lys532 side chain and the 5′ OH of the scissile phosphate is longer than the wild type enzyme, providing an atomic explanation for the reduced religation rate of the mutant. Taken together these results indicate the existence of a long range communication between the linker domain and the active site region and points out the crucial role of the linker in the modulation of the catalytic activity.     

The role of single-strand breaks in the catenation reaction catalyzed by the rat type I topoisomerase

The type I topoisomerase from rat cells produces true catenanes from circular SV40 DNA in a reaction which is dependent on the presence of a single-strand break in at least one member of a pair of reacting molecules. The role of the single-strand break in the reaction was examined. Molecules containing a nick with a 3'-hydroxyl and 5'-phosphate or a nick with a 3'-phosphate and 5'-hydroxyl and molecules with single-stranded gaps were all found to be equally effective in the catenation reaction. It was found that the enzyme could, at a low frequency, break DNA by acting opposite a pre-existing single-strand break. Thus, incubation of nicked circular DNA in the presence of the topoisomerase, polynucleotide kinase, and [gamma-32P]ATP led to the production of a low level of labeled linear molecules containing covalently attached protein. Nicked linear molecules treated with topoisomerase in the absence of polynucleotide kinase generated fragments of sizes consistent with breakage in the opposite strand near the pre-existing nick. Based on these results, we propose that the catenation reaction may involve the transient production of linear intermediates by the action of the topoisomerase opposite a pre-existing nick in the DNA. Rejoining of the two ends by the enzyme could lead to the interlocking of two or more circular DNAs. In addition, these results suggest a possible role for the type I topoisomerase in illegitimate recombination.     

Nick-containing oligonucleotides as human topoisomerase I inhibitors

A series of oligonucleotides with various lengths that contain nick and topoisomerase I-binding sites were designed. The interactions between these oligonucleotides and human topoisomerase I were investigated and the most efficient one among them has displayed IC₅₀ value of 6.3 nM. Our studies have also demonstrated that the position of the nick as well as the length of the oligonucleotides were crucial factors for the inhibition of this nuclear enzyme.     

Characterization of a camptothecin-resistant human DNA topoisomerase I

Topoisomerase I purified from a camptothecin-resistant human leukemia cell line and from the parental, camptothecin-sensitive line were compared in vitro. Relaxation of supercoiled DNA by the wild type enzyme was inhibited in the presence of camptothecin, while the mutant enzyme was unimpaired. Camptothecin altered the cleavage pattern of the wild type but not of the mutant enzyme. The stability of cleavable complexes was studied at a preferred topoisomerase I-binding sequence recognized by both enzymes. Camptothecin greatly enhanced the kinetic stability of the cleavable complex formed by the wild type enzyme, whereas that of the mutant enzyme was only marginally affected. In the absence of camptothecin, the cleavable complex formed by the mutant enzyme was stabilized relative to that of the wild type by several criteria. Thus, the mutant enzyme cleaved the topoisomerase I recognition sequence with 2-fold higher efficiency than the wild type enzyme. The mutant cleavable complex had a higher kinetic stability and was less sensitive to salt dissociation than the wild type complex. Furthermore, the mutant enzyme formed cleavable complexes in the absence of divalent cations, which were required for complex formation by the wild type enzyme.