We report the x-ray crystal structure of human topoisomerase I covalently joined to double-stranded DNA and bound to the clinically approved anticancer agent Topotecan. Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by intercalating between the upstream (؊1) and downstream (؉1) base pairs. Intercalation displaces the downstream DNA, thus preventing religation of the cleaved strand. By specifically binding to the enzyme-substrate complex, Topotecan acts as an uncompetitive inhibitor. The structure can explain several of the known structure-activity relationships of the camptothecin family of anticancer drugs and suggests that there are at least two classes of mutations that can produce a drug-resistant enzyme. The first class includes changes to residues that contribute to direct interactions with the drug, whereas a second class would alter interactions with the DNA and thereby destabilize the drug-binding site. Eukaryotic DNA topoisomerase I (topo I) is an enzyme that acts to relax supercoils generated during transcription and DNA replication (1). Because of the size of the eukaryotic chromosome, removal of these supercoils can only be accomplished locally by introducing breaks into the DNA helix. Topo I mediates DNA relaxation by creating a transient single-strand break in the DNA duplex. This transient nick allows the broken strand to rotate around its intact complement, effectively removing local supercoils. Strand nicking results from the transesterification of an active-site tyrosine (Tyr-723) at a DNA phosphodiester bond forming a 3Ј-phosphotyrosine covalent enzyme-DNA complex. After DNA relaxation, the covalent intermediate is reversed when the released 5Ј-OH of the broken strand reattacks the phosphotyrosine intermediate in a second transesterification reaction. The rate of religation is normally much faster than the rate of cleavage, and this ensures that the steady-state concentration of the covalent 3Ј-phosphotyrosyl topo I-DNA complex remains low (2).However, a variety of DNA lesions and drugs have been shown to stabilize the covalent 3Ј-phosphotyrosyl intermediate (3). For example, camptothecin (CPT) is a natural product that was originally discovered because of its antitumor activity (4) and was later demonstrated to cause the accumulation of topo I-DNA adducts in vitro and in vivo (5, 6). CPTs bind the covalent 3Ј-phosphotyrosyl intermediate and specifically block DNA religation (7), thus converting topo I into a DNA-damaging agent (8). Topo I is the sole intramolecular target of CPT, and the cytotoxic effects of CPT poisoning are S-phase specific (9). During DNA replication, the replication fork is thought to collide with the ''trapped'' topo I-DNA complexes, resulting in double-strand breaks and ultimately cell death (10).It has been difficult to study the mechanism of CPT activity because the drug acts as an uncompetitive inhibitor and binds only the transient covalent enzyme-substrate complex (7,11). To isolate the covalent topo I-DNA complex, we have used suicide DNA ...

Human topoisomerase I (top1) is the molecular target of a diverse set of anticancer compounds, including the camptothecins, indolocarbazoles, and indenoisoquinolines. These compounds bind to a transient top1-DNA covalent complex and inhibit the resealing of a single-strand nick that the enzyme creates to relieve superhelical tension in duplex DNA. (Hertzberg, R. P.; et al. Biochem. 1989, 28, 4629-4638. Hsiang, Y. H.; et al. J. Biol. Chem 1985, 260, 14873-14878. Champoux, J. J. Annu. Rev. Biochem. 2001, 70, 369-413. Stewart, L.; et al. Science 1998, 729, 1534-1541.) We report the X-ray crystal structures of the human top1-DNA complex bound with camptothecin and representative members of the indenoisoquinoline and indolocarbazole classes of top1 poisons. The planar nature of all three structurally diverse classes allows them to intercalate between DNA base pairs at the site of single-strand cleavage. All three classes of compounds have a free electron pair near Arg364, a residue that if mutated confers resistance to all three classes of drugs. The common intercalative binding mode is augmented by unexpected chemotype-specific contacts with amino acid residues Asn352 and Glu356, which adopt alternative side-chain conformations to accommodate the bound compounds. These new X-ray structures explain how very different molecules can stabilize top1-DNA covalent complexes and will aid the rational design of completely novel structural classes of anticancer drugs.

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The cytokine thrombopoietin (TPO), the ligand for the hematopoietic receptor c-Mpl, acts as a primary regulator of megakaryocytopoiesis and platelet production. We have determined the crystal structure of the receptor-binding domain of human TPO (hTPO 163) to a 2.5-Å resolution by complexation with a neutralizing Fab fragment. The backbone structure of hTPO 163 (1) predicted the existence of a potent, lineage-specific soluble factor, which they called thrombopoietin (TPO), that stimulates megakaryocytopoiesis and platelet production. It was not until 1994 that unequivocal evidence for the existence of this elusive molecule was provided by the nearly simultaneous isolation and cloning of TPO by five independent research groups (2-6). This cytokine has proven to be a primary factor in megakaryocytopoiesis from megakaryocyte colony formation to platelet production and the differentiation and proliferation of progenitor cells of multiple hematopoietic lineages (7). As such, TPO is being investigated for its potential to treat thrombocytopenia resulting from AIDS and chemotherapy and radiation treatments for cancer and leukemia and for the in vivo and ex vivo expansion of hematopoietic stem cells for bone marrow transplantation.Human TPO (hTPO) is a heavily glycosylated protein with two distinct regions. The 153-residue N-terminal region is homologous to human erythropoietin (EPO) with which it shares 23% sequence identity and is sufficient for receptor binding and signal transduction (2,3,8). The 179-residue C-terminal region has a large number of proline and glycine residues and six N-linked glycosylation sites. Its function is not known, although recent work indicates a role in secretion and protection from proteolysis (9, 10).The TPO receptor c-Mpl was first identified as an oncogene of the murine myeloproliferative leukemia virus (11, 12) that was able to immortalize hematopoietic progenitor cells and was later cloned from human and mouse (13,14). c-Mpl is expressed in some pluripotent hematopoietic stem cells (15) and in the megakaryocyte lineage from progenitor cells to platelets (16). It is a class I cytokine receptor of the hematopoietic superfamily of receptors and signals by the JAK͞STAT, Ras, and mitogenactivated protein kinase pathways (17-21). Class I hematopoietic receptors bind to their cytokine ligands by Ϸ200-aa Ig-like extracellular domains called cytokine receptor homology (CRH) or hematopoietic receptor domains that contain a distinctive WSXWS sequence motif (13).Cytokines possess two distinct interaction sites that bind with differing affinities [high affinity (nanomolar range) and low affinity (micromolar range)] to the same cytokinerecognition surface of the CRH domain. Crystal structures of human EPO and human growth hormone (hGH) in complex with the extracellular CRH domains of their receptors (22, 23) have shown the cytokine-CRH interaction in detail. However, unlike EPO receptor (EPOR) and hGH receptor (hGHR), which have only one CRH domain, c-Mpl belongs to a subset of hematopoietic ...

Escherichia coli glycerol kinase (EC 2.7.1.30; ATP:glycerol 3-phosphotransferase) is a key element in a signal transduction pathway that couples expression of genes required for glycerol metabolism to the relative availability of glycerol and glucose. Its catalytic activity is inhibited by protein-protein interactions with IIIglc, a phosphotransferase system protein, and by fructose 1,6-bisphosphate (FBP); each of these allosteric effectors constitutes a positive signal that glucose is available. Loss of glucose inhibition of glycerol metabolism was used to screen for regulatory mutants of glycerol kinase after hydroxylamine mutagenesis of the cloned glpK gene. Two mutant enzymes were identified and shown by DNA sequencing to contain the mutations alanine 65 to threonine (A65T) and aspartate 72 to asparagine (D72N). Initial velocity studies show the mutations do not significantly affect the catalytic properties, hence active-site structures, of the enzymes. Both mutations decrease inhibition by FBP; A65T eliminates the inhibition while D72N appears to decrease the affinity for FBP and the extent of the inhibition. However, neither mutation significantly affects inhibition by IIIglc. Gel-permeation chromatography studies show that both of the mutations alter the dimer-tetramer assembly reaction of the enzyme and the effect of FBP in increasing the molecular weight. The effects of the mutations on the assembly reaction are consistent with the locations of these two amino acid residues in the X-ray structure, which shows them to be associated with an alpha-helix that constitutes one of the two subunit-subunit interfaces within the tetramer.(ABSTRACT TRUNCATED AT 250 WORDS)

We conclude that the new tetramer structure presented here is an inactive form of the physiologically relevant tetramer. The structure and location of the orthophosphate-binding site is consistent with it being part of the FBP-binding site. Mutational analysis and the structure of the IIAGlc-GK(IIe474-->Asp) complex suggest the conformational transition of the IIAGlc-binding site to be an essential aspect of IIAGlc regulation.

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Stromal glycerol-3-phosphate acyltransferases (GPAT) are responsible for the selective incorporation of saturated and unsaturated fatty-acyl chains into chloroplast membranes, which is an important determinant of a plant's ability to tolerate chilling temperatures. The molecular mechanisms of plant chilling tolerance were elucidated by creating chimeric GPATs between squash (Cucurbita moscata, chilling-sensitive) and spinach (Spinacea oleracea, chilling-tolerant) and the results were interpreted using structural information on squash GPAT determined by X-ray crystallography at 1.55 A Ê resolution. Enzymatic analysis of the chimeric GPATs showed that the chimeric GPATs containing the spinach region from residues 128 to 187 prefer the 18:1 unsaturated fatty acid rather than 16:0 saturated fatty acid. Structure analysis suggests that the size and character of the cavity that is formed from this region determines the speci®c recognition of acyl chains.