Structural Basis for Lack of ADP-ribosyltransferase Activity in Poly(ADP-ribose) Polymerase-13/Zinc Finger Antiviral Protein

The mammalian poly(ADP-ribose) polymerase (PARP) family includes ADP-ribosyltransferases with diphtheria toxin homology (ARTD). Most members have mono-ADP-ribosyltransferase activity. PARP13/ARTD13, also called zinc finger antiviral protein, has roles in viral immunity and microRNA-mediated stress responses. PARP13 features a divergent PARP homology domain missing a PARP consensus sequence motif; the domain has enigmatic functions and apparently lacks catalytic activity. We used x-ray crystallography, molecular dynamics simulations, and biochemical analyses to investigate the structural requirements for ADP-ribosyltransferase activity in human PARP13 and two of its functional partners in stress granules: PARP12/ARTD12, and PARP15/BAL3/ARTD7. The crystal structure of the PARP homology domain of PARP13 shows obstruction of the canonical active site, precluding NAD⁺ binding. Molecular dynamics simulations indicate that this closed cleft conformation is maintained in solution. Introducing consensus side chains in PARP13 did not result in 3-aminobenzamide binding, but in further closure of the site. Three-dimensional alignment of the PARP homology domains of PARP13, PARP12, and PARP15 illustrates placement of PARP13 residues that deviate from the PARP family consensus. Introducing either one of two of these side chains into the corresponding positions in PARP15 abolished PARP15 ADP-ribosyltransferase activity. Taken together, our results show that PARP13 lacks the structural requirements for ADP-ribosyltransferase activity.     

Structural and biophysical characterization of human myo-inositol oxygenase

Altered inositol metabolism is implicated in a number of diabetic complications. The first committed step in mammalian inositol catabolism is performed by myo-inositol oxygenase (MIOX), which catalyzes a unique four-electron dioxygen-dependent ring cleavage of myo-inositol to D-glucuronate. Here, we present the crystal structure of human MIOX in complex with myo-inosose-1 bound in a terminal mode to the MIOX diiron cluster site. Furthermore, from biochemical and biophysical results from N-terminal deletion mutagenesis we show that the N terminus is important, through coordination of a set of loops covering the active site, in shielding the active site during catalysis. EPR spectroscopy of the unliganded enzyme displays a two-component spectrum that we can relate to an open and a closed active site conformation. Furthermore, based on site-directed mutagenesis in combination with biochemical and biophysical data, we propose a novel role for Lys(127) in governing access to the diiron cluster.     

Circular dichroism and saccharide-induced conformational transitions of lectins from Ricinus communis.

Conformational studies on lectins from castor beans (Ricinus communis), RCA_I and RCA_II, were performed by using circular dichroism (CD). The CD spectra were similar showing several negative bands at 270–320 nm, a positive region at 230–250 nm, several negative bands at 205–225 nm, and a positive peak at about 195 nm. However, significant differences were observed in the band strength between RCA_I and RCA_II. Lactose, melibiose, and d-fucose induced marked Conformational alterations in RCA_I, whereas weaker effects were produced by d-galactose and l-rhamnose. Saccharide-induced conformational alterations were weaker in RCA_II than in RCA_I, with only lactose and melibiose inducing significant alterations. d-Glucose and 2-acetamido-2-deoxy-d-glucose, which do not inhibit hemagglutination by RCA_I or RCA_II, did not influence lectin conformation. Acetylation of tyrosyl groups with N-acetylimidazole produced changes in the CD bands in the near uv indicating involvement of tyrosine residues. The saccharide effect was most pronounced at 285 nm, a band that was assigned to a tyrosine chromophore. Analysis of the CD bands in the far-uv zone indicated the presence of approximately 50% pleated sheet (β) structure, and 13–15% α-helix in both RCA_I and RCA_II. According to the CD results, the polypeptide chain backbone in the lectins was not affected by the saccharides, whereas significant disorganization occurred in 7 m guanidine-HCl.     

Estrogen receptor beta-subtype selective tetrahydrofluorenones: use of a fused pyrazole as a phenol bioisostere

Synthesis of a series of fused pyrazole tetrahydrofluorenone analogs which are potent, ERbeta subtype selective ligands is described. Analogs possessing subnanomolar ERbeta binding, greater than 100-fold ERbeta-selectivity, and oral bioavailability are reported.     

Comparative Structural Analysis of Human DEAD-Box RNA Helicases

DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.     

Recognition of Mono-ADP-Ribosylated ARTD10 Substrates by ARTD8 Macrodomains

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Highlights? ARTD8 macrodomains read ARTD10-dependent mono-ADP-ribosylation ? The structure of ARTD8 macrodomains reveals a conserved fold for ADP-ribose binding ? Distinct macrodomains read mono- and poly-ADP-ribosylation selectively ? ARTD8 macrodomains can be used to visualize mono-ADP-ribosylation in cells     

Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors

Inhibitors of poly-ADP-ribose polymerase (PARP) family proteins are currently in clinical trials as cancer therapeutics, yet the specificity of many of these compounds is unknown. Here we evaluated a series of 185 small-molecule inhibitors, including research reagents and compounds being tested clinically, for the ability to bind to the catalytic domains of 13 of the 17 human PARP family members including the tankyrases, TNKS1 and TNKS2. Many of the best-known inhibitors, including TIQ-A, 6(5H)-phenanthridinone, olaparib, ABT-888 and rucaparib, bound to several PARP family members, suggesting that these molecules lack specificity and have promiscuous inhibitory activity. We also determined X-ray crystal structures for five TNKS2 ligand complexes and four PARP14 ligand complexes. In addition to showing that the majority of PARP inhibitors bind multiple targets, these results provide insight into the design of new inhibitors.     

Cell surface expression by adult rat hepatocytes of a non-collagen glycoprotein present in rat liver biomatrix

A rabbit antiserum raised against ACI rat liver biomatrix was used to identify components common to biomatrix and plasma membranes of adult hepatocytes. Biomatrix was isolated from intact rat livers by reverse perfusion via the inferior vena cava with sodium deoxycholate, nucleases and lipid extracting solvents. Immunoprecipitation analysis of detergent extracts of hepatocytes surface-labeled with 125I indicated that antibodies, purified from anti- biomatrix antiserum by adsorption and desorption from intact hepatocytes, showed reactivity with a single MW 105 kD component, designated Hep 105. Indirect immunofluorescence analysis showed that Hep 105 was expressed in some regions of the perisinusoidal space and in all three domains of the hepatocyte plasma membrane and was present on some but not all of the fibrous elements in frozen sections of biomatrix . The presence of Hep 105 on biomatrix was confirmed by immunoprecipitation analysis which showed that Hep 105 was present in components solubilized from biomatrix by sequential treatment with 0.5 M acetic acid, 0.05% collagenase and 4 M urea. Further characterization using immunoprecipitation analysis in combination with immobilized lectins and two-dimensional polyacrylamide gel electrophoresis (PAGE) indicated that Hep 105 was a non-collagen glycoprotein which showed charge heterogeneity and existed on the cell surface as a disulfide-linked heterodimer of apparent MW 125 kD. Two hybridomas, constructed by fusing P3 X 63Ag8 myeloma cells with spleen cells from mice immunized with intact hepatocytes, were shown by immunodepletion and two-dimensional gel electrophoretic analysis to be secreting monoclonal antibodies (Mab) against Hep 105. Examination of frozen sections of rat liver stained by indirect immunofluorescence showed that reactivity of both Mabs was concentrated in the bile canalicular domain of the hepatocyte plasma membrane, suggesting that the reactive epitopes were not accessible in the sinusoidal and intercellular membrane domains. Taken together, these results suggest that Hep 105 may play a role in the interactions between hepatocytes and extracellular matrix.