Structure of FcγRI in complex with Fc reveals the importance of glycan recognition for high-affinity IgG binding

Fc gamma receptor I (FcγRI) contributes to protective immunity against bacterial infections, but exacerbates certain autoimmune diseases. The sole high-affinity IgG receptor, FcγRI plays a significant role in immunotherapy. To elucidate the molecular mechanism of its high-affinity IgG binding, we determined the crystal structure of the extracellular domains of human FcγRI in complex with the Fc domain of human IgG₁. FcγRI binds to the Fc in a similar mode as the low-affinity FcγRII and FcγRIII receptors. In addition to many conserved contacts, FcγRI forms additional hydrogen bonds and salt bridges with the lower hinge region of Fc. Unique to the high-affinity receptor-Fc complex, however, is the conformation of the receptor D2 domain FG loop, which enables a charged KHR motif to interact with proximal carbohydrate units of the Fc glycans. Both the length and the charge of the FcγRI FG loop are well conserved among mammalian species. Ala and Glu mutations of the FG loop KHR residues showed significant contributions of His-174 and Arg-175 to antibody binding, and the loss of the FG loop–glycan interaction resulted in an ∼20- to 30-fold decrease in FcγRI affinity to all three subclasses of IgGs. Furthermore, deglycosylation of IgG₁ resulted in a 40-fold loss in FcγRI binding, demonstrating involvement of the receptor FG loop in glycan recognition. These results highlight a unique glycan recognition in FcγRI function and open potential therapeutic avenues based on antibody glycan engineering or small molecular glycan mimics to target FcγRI for certain autoimmune diseases.IgGs and pentraxins are circulating immune components that directly recognize pathogens. On formation of immune complexes or opsonization, they activate cellular response through Fc receptors (FcRs) (1, 2). The FcRs for IgGs include FcγRI (CD64); FcγRII (CD32) with A, B, and C isoforms; and FcγRIII (CD16) with two isoforms (3). Most of these are activating receptors either containing an intracellular immunoreceptor tyrosine-based activation motif or associated with an FcR common γ chain (4). FcγRIIB is an inhibitory receptor that contains an intracellular immunoreceptor tyrosine-based inhibitory motif. FcγRIIIB does not have a cytosolic domain and is anchored to the plasma membrane through glycosylphosphatidylinositol linkage. The binding affinity to IgG ranges from 10⁻⁸ M for FcγRI to 10⁻⁵–10⁻⁷ M for FcγRII and III (3).FcγRI plays an important role in the protection against bacterial infections, but also exacerbates certain autoimmune diseases (5). Owing to its high-affinity antibody binding, FcγRI is important in antibody therapy as well (6, 7). To date, the structure of the ligand-bound high-affinity receptor has not been determined, however. Consequently, the mechanism of its high-affinity antibody recognition remains to be elucidated. The role of glycan in antibody function has been a subject of intense study. Differential glycosylation of Fc, notably fucosylated Fc, is known to affect Fc receptor binding (8, 9). Furthermore, sialylated IgGs have been shown to be anti-inflammatory components of intravenous immunoglobulin (10, 11), and glycosylation affects their binding to the low-affinity FcγRIIB and FcγRIII (11–13). Structural evidence suggests that the conserved glycosylation at Asn-297 of the constant region of IgG₁ is important to maintain the conformation of Fc for receptor binding (12, 14). Whether Fc receptors make significant glycan contacts for their IgG affinity is not clear, however.Structures of the low-affinity Fcγ receptors have been determined with bound IgG-Fc (15–18). Unlike the other two-domain FcγRs, FcγRI contains three extracellular Ig-like domains, designated D1, D2, and D3. Earlier mutational analysis suggests that D2 and D3 domains are important to confer high-affinity antibody binding (19). Recently, the structure of human FcγRI showed a close packing of the FcγRI D1 and D2 domains resembling that of FcεRI, and mutations in the FG loop of the FcγRI D2 domain reduced its IgG binding affinity (20). The mechanism of the high-affinity FcγRI ligand recognition remains unresolved. To provide further insight into the high-affinity antibody recognition by FcγRI, and to facilitate the development of FcγRI-mediated immunotherapy, we determined the structure of the extracellular domains of human FcγRIA in complex with the Fc domain of human IgG₁. Our study identifies a structural mechanism for high-affinity IgG binding by the receptor.     

Aggregation of γ-crystallins associated with human cataracts via domain swapping at the C-terminal β-strands

The prevalent eye disease age-onset cataract is associated with aggregation of human γD-crystallins, one of the longest-lived proteins. Identification of the γ-crystallin precursors to aggregates is crucial for developing strategies to prevent and reverse cataract. Our microseconds of atomistic molecular dynamics simulations uncover the molecular structure of the experimentally detected aggregation-prone folding intermediate species of monomeric native γD-crystallin with a largely folded C-terminal domain and a mostly unfolded N-terminal domain. About 30 residues including a, b, and c strands from the Greek Key motif 4 of the C-terminal domain experience strong solvent exposure of hydrophobic residues as well as partial unstructuring upon N-terminal domain unfolding. Those strands comprise the domain-domain interface crucial for unusually high stability of γD-crystallin. We further simulate the intermolecular linkage of these monomeric aggregation precursors, which reveals domain-swapped dimeric structures. In the simulated dimeric structures, the N-terminal domain of one monomer is frequently found in contact with residues 135-164 encompassing the a, b, and c strands of the Greek Key motif 4 of the second molecule. The present results suggest that γD-crystallin may polymerize through successive domain swapping of those three C-terminal β-strands leading to age-onset cataract, as an evolutionary cost of its very high stability. Alanine substitutions of the hydrophobic residues in those aggregation-prone β-strands, such as L145 and M147, hinder domain swapping as a pathway toward dimerization. These findings thus provide critical molecular insights onto the initial stages of age-onset cataract, which is important for understanding protein aggregation diseases.     

Tunable recognition of the steroid α-face by adjacent π-electron density

We report a previously unknown recognition motif between the α-face of the steroid hydrocarbon backbone and π-electron-rich aromatic substrates. Our study is based on a systematic and comparative analysis of the solid-state complexation of four steroids with 24 aromatic molecules. By using the solid state as a medium for complexation, we circumvent solubility and solvent competition problems that are inherent to the liquid phase. Characterization is performed using powder and single crystal X-ray diffraction, infrared solid-state spectroscopy and is complemented by a comprehensive cocrystal structure prediction methodology that surpasses earlier computational approaches in terms of realism and complexity. Our combined experimental and theoretical approach reveals that the α⋯π stacking is of electrostatic origin and is highly dependent on the steroid backbone’s unsaturated and conjugated character. We demonstrate that the α⋯π stacking interaction can drive the assembly of molecules, in particular progesterone, into solid-state complexes without the need for additional strong interactions. It results in a marked difference in the solid-state complexation propensities of different steroids with aromatic molecules, suggesting a strong dependence of the steroid-binding affinity and even physicochemical properties on the steroid’s A-ring structure. Hence, the hydrocarbon part of the steroid is a potentially important variable in structure-activity relationships for establishing the binding and signaling properties of steroids, and in the manufacture of pharmaceutical cocrystals.     

Structural basis of UGUA recognition by the Nudix protein CFIm25 and implications for a regulatory role in mRNA 3′ processing

Human Cleavage Factor Im (CFI_m) is an essential component of the pre-mRNA 3′ processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI_m25) of the CFI_m complex possesses a characteristic α/β/α Nudix fold, CFI_m25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI_m25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI_m25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson–Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap₄A (diadenosine tetraphosphate) by CFI_m25 suggests a potential role for small molecules in the regulation of mRNA 3′ processing.     

Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-? structure of the ternary complex

Factor (f) IXa is a critical enzyme for the formation of stable blood clots, and its deficiency results in hemophilia. The enzyme functions at the confluence of the intrinsic and extrinsic pathways by binding to fVIIIa and rapidly generating fXa. In spite of its importance, little is known about how fIXa recognizes its cofactor, its substrate, or its only known inhibitor, antithrombin (AT). However, it is clear that fIXa requires extensive exosite interactions to present substrates for efficient cleavage. Here we describe the 1.7-Å crystal structure of fIXa in its recognition (Michaelis) complex with heparin-activated AT. It represents the highest resolution structure of both proteins and allows us to address several outstanding issues. The structure reveals why the heparin-induced conformational change in AT is required to permit simultaneous active-site and exosite interactions with fIXa and the nature of these interactions. The reactive center loop of AT has evolved to specifically inhibit fIXa, with a P2 Gly so as not to clash with Tyr99 on fIXa, a P4 Ile to fit snugly into the S4 pocket, and a C-terminal extension to exploit a unique wall-like feature of the active-site cleft. Arg150 is at the center of the exosite interface, interacting with AT residues on β-sheet C. A surprising crystal contact is observed between the heparin pentasaccharide and fIXa, revealing a plausible mode of binding that would allow longer heparin chains to bridge the complex.     

Species-specific factors mediate extensive heterogeneity of mRNA 3′ ends in yeasts

Most eukaryotic genes express mRNAs with alternative polyadenylation sites at their 3′ ends. Here we show that polyadenylated 3′ termini in three yeast species (Saccharomyces cerevisiae, Kluyveromyces lactis, and Debaryomyces hansenii) are remarkably heterogeneous. Instead of a few discrete 3′ ends, the average yeast gene has an “end zone,” a >200 bp window with >60 distinct poly(A) sites, the most used of which represents only 20% of the mRNA molecules. The pattern of polyadenylation within this zone varies across species, with D. hansenii possessing a higher focus on a single dominant point closer to the ORF terminus. Some polyadenylation occurs within mRNA coding regions with a strong bias toward the promoter. The polyadenylation pattern is determined by a highly degenerate sequence over a broad region and by a local sequence that relies on A residues after the cleavage point. Many dominant poly(A) sites are predicted to adopt a common secondary structure that may be recognized by the cleavage/polyadenylation machinery. We suggest that the end zone reflects a region permissive for polyadenylation, within which cleavage occurs preferentially at the A-rich sequence. In S. cerevisiae strains, D. hansenii genes adopt the S. cerevisiae polyadenylation profile, indicating that the polyadenylation pattern is mediated primarily by species-specific factors.     

Anabolic action of parathyroid hormone regulated by the β2-adrenergic receptor

Parathyroid hormone (PTH), the major calcium-regulating hormone, and norepinephrine (NE), the principal neurotransmitter of sympathetic nerves, regulate bone remodeling by activating distinct cell-surface G protein-coupled receptors in osteoblasts: the parathyroid hormone type 1 receptor (PTHR) and the β(2)-adrenergic receptor (β(2)AR), respectively. These receptors activate a common cAMP/PKA signal transduction pathway mediated through the stimulatory heterotrimeric G protein. Activation of β(2)AR via the sympathetic nervous system decreases bone formation and increases bone resorption. Conversely, daily injection of PTH (1-34), a regimen known as intermittent (i)PTH treatment, increases bone mass through the stimulation of trabecular and cortical bone formation and decreases fracture incidences in severe cases of osteoporosis. Here, we show that iPTH has no osteoanabolic activity in mice lacking the β(2)AR. β(2)AR deficiency suppressed both iPTH-induced increase in bone formation and resorption. We showed that the lack of β(2)AR blocks expression of iPTH-target genes involved in bone formation and resorption that are regulated by the cAMP/PKA pathway. These data implicate an unexpected functional interaction between PTHR and β(2)AR, two G protein-coupled receptors from distinct families, which control bone formation and PTH anabolism.     

Assessment of the Clinical Significance of Production of Extended-spectrum β-Lactamases (ESBL) by Enterobacteriaceae

Abstract Background: We conducted a retrospective, cohort-controlled study to evaluate the effect of extended-spectrum β-lactamase (ESBL) production by Enterobacteriaceae isolated from blood cultures, and of third or fourth generation cephalosporin treatment, on outcome. Methods: Four hundred and fifty patient-unique Enterobacteriaceae, isolated from blood cultures during 2000 (before routine ESBL testing was introduced), were tested for ESBL by double-disk method and by E-test, assessing cefotaxime, ceftazidime and cefpodoxime, with and without clavulanate. Cases consisted of ESBL-positive (+) samples, originally reported as ceftazidime-susceptible; controls were ESBL-negative (–). Patient records were extensively reviewed. Results: We identified 68 Enterobacteriaceae that were ESBL(+); they were compared with 186 ESBL(–) control organisms. Patients with sepsis due to an ESBL(+) organism more often had nosocomial infection, resided in nursing homes, were functionally dependent, had an indwelling catheter, had Klebsiella, and had a lower serum albumin level (all p < 0.001). Survival of patients with ESBL(+) and ESBL(–) sepsis was, respectively, 71% and 84% (p < 0.05). Multivariate analysis revealed that the only independent risk factor for death was a low serum albumin. Neither empiric nor definite treatment with cephalosporins was found to be an independent risk factor for death. Subset analysis was conducted on 15 patients with ESBL(+) sepsis and 21 controls with ESBL(–) sepsis, who had been treated with ceftazidime or cefepime only. In this subset, ESBL(+) patients more often resided in nursing homes (< 0.05), they had a significantly lower APACHE-II score (< 0.01) and the infection was more often nosocomial (< 0.005). Survival of ESBL(+) and ESBL(–) patients was 67% and 71%, respectively (NS). Time till defervescence did not differ between cases and controls. Conclusion: Mortality of patients with ESBL(+) sepsis was higher than that of patients with ESBL(–) sepsis. The reason appears to be related to other factors rather than to empiric treatment with cephalosporins or the nature or resistance pattern of the organism. This, at least, appears to be the case for patients with urosepsis, who constituted the majority of patients in this study.     

Inhibition of the β-barrel assembly machine by a peptide that binds BamD

The protein complex that assembles integral membrane β-barrel proteins in the outer membranes of Gram-negative bacteria is an attractive target in the development of new antibiotics. This complex, the β-barrel assembly machine (Bam), contains two essential proteins, BamA and BamD. We have identified a peptide that inhibits the assembly of β-barrel proteins in vitro by characterizing the interaction of BamD with an unfolded substrate protein. This peptide is a fragment of the substrate protein and contains a conserved amino acid sequence. We have demonstrated that mutations of this sequence in the full-length substrate protein impair the protein’s assembly, implying that BamD’s interaction with this sequence is an important part of the assembly mechanism. Finally, we have found that in vivo expression of a peptide containing this sequence causes growth defects and sensitizes Escherichia coli to antibiotics to which they are normally resistant. Therefore, inhibiting the binding of substrates to BamD is a viable strategy for developing new antibiotics directed against Gram-negative bacteria.Membrane proteins with β-barrel structure are found in the outer membranes (OMs) of Gram-negative bacteria and in the mitochondria and chloroplasts of eukaryotes. These proteins are assembled into their native membranes by conserved protein complexes, which contain a β-barrel protein of the outer membrane protein 85 (Omp85) family and some number of accessory proteins (1–6). β-barrel assembly is an essential process and, as such, is an attractive target for the development of new antibiotics that could kill Gram-negative pathogens. However, the mechanism by which β-barrel assembly proceeds is only beginning to be elucidated. Structures of the components of the bacterial β-barrel assembly machine (BamA–E) have been determined recently, and several hypotheses about how they facilitate the assembly of its substrates have been proposed (7–17). The β-barrel component BamA contains a kinked β-strand, which might allow substrate proteins to be inserted by passing laterally from the lumen of the BamA β-barrel into the hydrophobic membrane (18). BamA also contains a large soluble domain in addition to its integral β-barrel; this region extends into the periplasmic space between the inner membrane and OM and consists of five polypeptide transport-associated (POTRA) domains (19). The POTRA domains bind the other four components of the assembly complex, BamB–E, which are lipoproteins. Structural and biochemical studies have suggested that the POTRA domains, BamB, and BamD may interact with substrate proteins during their assembly (13, 15, 19–22). However, more detailed information is required about the nature of those interactions and whether they are critical in the assembly process to develop an integrated mechanistic model.Only two components of the Bam complex, BamA and BamD, are essential for Escherichia coli viability (2, 23). BamD is found in all proteobacteria (24, 25), but it bears no obvious homology to any of the accessory components of the mitochondrial or chloroplastic complexes. It is therefore unclear what its essential function is and whether that function is specific to bacteria. Do the β-barrel assembly complexes in all species use the same mechanism (perhaps with different accessory proteins), or have they evolved different essential components to meet their organism-specific requirements? We have previously demonstrated that BamD binds to two unfolded OMP substrates, OmpA and BamA, and that it directly facilitates the assembly of BamA (21). In this study, we have characterized this interaction to understand its role in the assembly process carried out by the complete Bam complex and to assess whether interfering with the binding of substrates to BamD might be a viable strategy for developing new antibiotics.     

CRYPTOCHROME-mediated phototransduction by modulation of the potassium ion channel β-subunit redox sensor

Blue light activation of the photoreceptor CRYPTOCHROME (CRY) evokes rapid depolarization and increased action potential firing in a subset of circadian and arousal neurons in Drosophila melanogaster. Here we show that acute arousal behavioral responses to blue light significantly differ in mutants lacking CRY, as well as mutants with disrupted opsin-based phototransduction. Light-activated CRY couples to membrane depolarization via a well conserved redox sensor of the voltage-gated potassium (K⁺) channel β-subunit (Kvβ) Hyperkinetic (Hk). The neuronal light response is almost completely absent in hk^−/− mutants, but is functionally rescued by genetically targeted neuronal expression of WT Hk, but not by Hk point mutations that disable Hk redox sensor function. Multiple K⁺ channel α-subunits that coassemble with Hk, including Shaker, Ether-a-go-go, and Ether-a-go-go–related gene, are ion conducting channels for CRY/Hk-coupled light response. Light activation of CRY is transduced to membrane depolarization, increased firing rate, and acute behavioral responses by the Kvβ subunit redox sensor.CRYPTOCHROME (CRY) is a photoreceptor that mediates rapid membrane depolarization and increased spontaneous action potential firing rate in response to blue light in arousal and circadian neurons in Drosophila melanogaster (1, 2). CRY regulates circadian entrainment by targeting circadian clock proteins to proteasomal degradation in response to light (3–6). CRY is expressed in a small subset of central brain circadian, arousal, and photoreceptor neurons in D. melanogaster and other insects, including the large lateral ventral neuron (LNv; l-LNv) subset (1, 2, 7, 8). The l-LNvs are light-activated arousal neurons (1, 2, 9–11), whereas the small lateral ventral neurons (s-LNvs) are critical for circadian function (5, 12). Previous results suggest that light activated arousal is likely attenuated in cry-null mutants. In addition to modulating light-activated firing rate, membrane excitability in the LNv neurons helps maintain circadian rhythms (9, 13, 14), and LNv firing rate is circadian regulated (2, 16).Based on our previous work suggesting that l-LNv electrophysiological light response requires a flavin-specific redox reaction and modulation of membrane K⁺ channels, we investigated the molecular mechanism for CRY phototransduction to determine how light-activated CRY is coupled to rapid membrane electrical changes. Sequence and structural data suggest that the cytoplasmic Kvβs are redox sensors based on a highly conserved aldo-keto-reductase domain (AKR) (17–21). Although no functional role for redox sensing by Kvβ subunits has been established yet in vivo, studies with heterologously expressed WT and mutant Kvβ subunits show that they confer modulatory sensitivity to coexpressed K⁺ channels in response to oxidizing and reducing chemical agents (22–24). Mammals express six Kvβ genes, whereas Drosophila expresses a single Kvβ designated HYPERKINETIC (Hk) (18). We find that the light-activated redox reaction of the flavin adenine dinucleotide (FAD) chromophore in CRY has a distinct phototransduction mechanism that evokes membrane electrical responses via the Kvβ subunit Hk, which we show is a functional redox sensor in vivo.     

Electrophysiological effects mediated by the stimulation of cardiac β2-adrenoceptors with tulobuterol

Summary We studied the electrophysiological effects of the specific ₂-agonist tulobuterol in the guinea-pig sinus node and in sheep cardiac Purkinje fibers. Stimulation of ₂-adrenoceptors by tulobuterol resulted in a slight increase in the rate of firing of the sinus node. In Purkinje fibers, however, automaticity was not affected up to concentrations of 10^–6 M. Consistently, tulobuterol (10^–8–10^–6 M) did not affect the pacemaker current studied under voltage-clamp conditions. In the same range of concentrations (10^–8–10^–6 M) tulobuterol dose-dependently increased the contractile force of driven Purkinje fibers. Tulobuterol, at a very high concentration (10^–5 M), had membrane depressant effects as demonstrated by the block of automaticity induced in the spontaneously beating Purkinje fibers and by the reduction of the maximum rate of depolarization in driven preparations.Our results suggest that stimulation of ₂-adrenoceptors with tulobuterol in sheep Purkinje fibers is associated with an inotropic rather than a chronotropic effect. On the whole, the data confirm the lack of cardiac side effects of tulobuterol.     

Assessing the severity of the small inframe deletion mutation in the α-subunit of β-hexosaminidase A found in the Turkish population by reproducing it in the more stable β-subunit

GM(2) gangliosidoses are a group of panethnic lysosomal storage diseases in which GM(2) ganglioside accumulates in the lysosome due to a defect in one of three genes, two of which encode the alpha- or beta-subunits of beta- N -acetylhexosaminidase (Hex) A. A small inframe deletion mutation in the catalytic domain of the alpha-subunit of Hex has been found in five Turkish patients with infantile Tay-Sachs disease. To date it has not been detected in other populations and is the only mutation to be found in exon 10. It results in detectable levels of inactive alpha-protein in its precursor form. Because the alpha- and beta-subunits share 60% sequence identity, the Hex A and Hex B genes are believed to have arisen from a common ancestral gene. Thus the subunits must share very similar three-dimensional structures with conserved functional domains. Hex B, the beta-subunit homodimer is more stable than the heterodimeric Hex A, and much more stable than Hex S, the alpha homodimer. Thus, mutations that completely destabilize the alpha-subunit can often be partially rescued if expressed in the aligned positions in the beta-subunit. To better understand the severity of the Turkish HEXA mutation, we reproduced the 12 bp deletion mutation (1267-1278) in the beta-subunit cDNA. Western blot analysis of permanently transfected CHO cells expressing the mutant detected only the pro-form of the beta-subunit coupled with a total lack of detectable Hex B activity. These data indicate that the deletion of the four amino acids severely affects the folding of even the more stable beta-subunit, causing its retention in the endoplasmic reticulum and ultimate degradation.     

Structural insight into the molecular mechanism of allosteric activation of human cystathionine β-synthase by S-adenosylmethionine

Cystathionine β-synthase (CBS) is a heme-dependent and pyridoxal-5′-phosphate–dependent protein that controls the flux of sulfur from methionine to cysteine, a precursor of glutathione, taurine, and H₂S. Deficiency of CBS activity causes homocystinuria, the most frequent disorder of sulfur amino acid metabolism. In contrast to CBSs from lower organisms, human CBS (hCBS) is allosterically activated by S-adenosylmethionine (AdoMet), which binds to the regulatory domain and triggers a conformational change that allows the protein to progress from the basal toward the activated state. The structural basis of the underlying molecular mechanism has remained elusive so far. Here, we present the structure of hCBS with bound AdoMet, revealing the activated conformation of the human enzyme. Binding of AdoMet triggers a conformational change in the Bateman module of the regulatory domain that favors its association with a Bateman module of the complementary subunit to form an antiparallel CBS module. Such an arrangement is very similar to that found in the constitutively activated insect CBS. In the presence of AdoMet, the autoinhibition exerted by the regulatory region is eliminated, allowing for improved access of substrates to the catalytic pocket. Based on the availability of both the basal and the activated structures, we discuss the mechanism of hCBS activation by AdoMet and the properties of the AdoMet binding site, as well as the responsiveness of the enzyme to its allosteric regulator. The structure described herein paves the way for the rational design of compounds modulating hCBS activity and thus transsulfuration, redox status, and H₂S biogenesis.Cystathionine β-synthase (CBS; EC 4.2.1.22) is a pyridoxal-5′-phosphate (PLP)-dependent enzyme that catalyzes the β-replacement of the hydroxyl group of l-serine (Ser) by l-homocysteine (Hcy), yielding cystathionine (Cth) (1). A deficient activity of human CBS (hCBS) is the cause of classical homocystinuria [CBS-deficient homocystinuria (CBSDH); Online Mendelian Inheritance in Man (OMIM) no. 236200], an autosomal, recessive inborn error of sulfur amino acid metabolism, characterized by increased levels of Hcy in plasma and urine. CBSDH manifests as a combination of connective tissue defects, skeletal deformities, vascular thrombosis, and mental retardation (2).The hCBS is a homotetrameric enzyme whose subunits are organized into three structural domains. The N-terminal region binds heme and is thought to function in redox sensing and/or enzyme folding (3, 4). The central catalytic core shows the fold of the type II family PLP-dependent enzymes (5, 6). Finally, the C-terminal region consists of a tandem pair of CBS motifs (7–9) that bind S-adenosylmethionine (AdoMet) and lead to an increase in catalytic activity by up to fivefold (10, 11). The CBS motif pair, commonly known as a “Bateman module” (12, 13), is responsible for CBS subunit tetramerization (14, 15). The presence of pathogenic missense mutations in this region often does not impair enzyme activity but typically interferes with binding of AdoMet and/or the enzyme’s activation by AdoMet (15–17). Removal of the regulatory region leads to a dimer with much increased activity (14, 15). Recently, we showed that removal of residues 516–525, forming a flexible loop of the CBS2 motif of hCBS, yields dimeric species (hCBSΔ516–525) with intact AdoMet binding capacity and activity responsiveness to AdoMet similar to a native hCBS WT (18).hCBS is regulated by a complex molecular mechanism that remains poorly understood. More than a decade ago, we and others hypothesized that hCBS might exist in two different conformations: a “basal” state with low activity, where the C-terminal regulatory domain would restrict the access of substrates into the catalytic site, and an AdoMet-bound “activated” state, where the AdoMet-induced conformational change would allow for enzyme activation (16, 19). Recently, we have unveiled the relative orientations of the regulatory and catalytic domains in hCBS (18), which were in a striking contrast to those of both the previous in silico models (20, 21) and the Drosophila melanogaster (dCBS) structure (22). Our data showed that, although the pairing mode and the orientation of catalytic cores are similar in both insect dCBS and hCBS, the position of their regulatory domains is markedly different (18). In the basal state, the Bateman modules from each hCBS unit are far apart and do not interact with each other, being placed just above the entrance of the catalytic site of the complementary subunit, thus hampering the access of substrates into this cavity. Our hCBSΔ516–525 structure additionally revealed the presence of two major cavities in the Bateman module, S1 and S2, one of which (S2) is solvent-exposed and probably represents the primary binding site for AdoMet (18). These findings are in agreement with the much higher basal activity of dCBS and its inability to bind or to be regulated by AdoMet (23, 24) and suggest that the structural basis underlying the regulation of the human enzyme markedly differs from CBS regulation in insects or yeast (24). Taken together, the available data indicate that binding of AdoMet to the Bateman module weakens the interaction between the regulatory domain and the catalytic core although the mechanism and the magnitude of the underlying structural effect are still under debate (16, 19, 25–27).To solve the molecular mechanism of hCBS regulation by AdoMet, we have analyzed the crystals of an engineered hCBSΔ516–525 protein that bears the mutation E201S, which potentially weakens and/or disrupts the interaction between the Bateman module and the catalytic core (Fig. 1A), thus favoring the activation of the enzyme. The data presented here fill a long-sought structural gap by unraveling the crystal structure of AdoMet-bound hCBS, thus providing the overall fold of the enzyme in its activated conformation and the identity of the AdoMet binding sites. Comparison with the structures of hCBS in basal conformation and constitutively activated dCBS was instrumental in the understanding of the regulatory role played by the C-terminal domain as well as the effect of some of the pathogenic mutations in the activation and/or inhibition of this key molecule of transsulfuration.Open in a separate windowFig. 1.Interactions between protein domains in basal hCBS. (A) In hCBSΔ516–525, residues Y484, N463, and S466 anchor the Bateman module (blue) to the protein core (gray) through H-bonds with the residues E201 and D198 from the loop L191–202, thus occluding the entrance to the catalytic pocket. (B) The CBS-specific activity of selected hCBS variants in the absence (blue bars) and the presence (red bars) of 300 µM AdoMet. hCBS enzyme species marked with “Δ” lack residues 516–525 and form dimers.     

Molecular mechanisms for the regulation of histone mRNA stem-loop–binding protein by phosphorylation

Replication-dependent histone mRNAs end with a conserved stem loop that is recognized by stem-loop–binding protein (SLBP). The minimal RNA-processing domain of SLBP is phosphorylated at an internal threonine, and Drosophila SLBP (dSLBP) also is phosphorylated at four serines in its 18-aa C-terminal tail. We show that phosphorylation of dSLBP increases RNA-binding affinity dramatically, and we use structural and biophysical analyses of dSLBP and a crystal structure of human SLBP phosphorylated on the internal threonine to understand the striking improvement in RNA binding. Together these results suggest that, although the C-terminal tail of dSLBP does not contact the RNA, phosphorylation of the tail promotes SLBP conformations competent for RNA binding and thereby appears to reduce the entropic penalty for the association. Increased negative charge in this C-terminal tail balances positively charged residues, allowing a more compact ensemble of structures in the absence of RNA.Histone synthesis increases at the beginning of S-phase to package newly replicated DNA with histone proteins, but synthesis must be shut down rapidly and histone mRNA degraded at the end of DNA replication because of the toxicity of surplus histone proteins (1, 2). This cyclic demand for histones requires strict regulation, which is achieved mainly by controlling the synthesis and degradation of histone mRNA (3). Replication-dependent histone mRNAs are the only known cellular mRNAs that are not polyadenylated and instead end with a conserved stem loop (4). Histone mRNAs are generated from longer histone pre-mRNAs as a result of an endonucleolytic cleavage between the stem loop and a purine-rich downstream sequence termed the “histone downstream element” (HDE) (5).Stem-loop–binding protein (SLBP), also known as “hairpin-binding protein” (6), binds to the histone mRNA stem loop, and U7 small nuclear ribonucleoprotein binds to the HDE (7). Other factors, including the endonuclease CPSF-73, are involved in both polyadenylation and histone mRNA 3′-end processing (8–11). In mammalian nuclear extracts, SLBP is not absolutely required for the biochemical reaction of processing (12). In contrast, cleavage of histone pre-mRNA in Drosophila cells and nuclear extracts requires the binding of SLBP to the stem loop (10, 13).The minimal histone mRNA processing domain of Drosophila SLBP contains a 72-aa RNA-binding domain (RBD) unique to SLBPs and an 18-aa C-terminal region (Fig. 1A) (14). This RNA-processing domain (RPD) is necessary and sufficient for histone mRNA 3′-end processing in vitro (15). The RBDs of human SLBP (hSLBP) and Drosophila SLBP (dSLBP) are phosphorylated at a Thr residue in a conserved TPNK motif (16, 17). The recent crystal structure of hSLBP RBD in complex with histone mRNA stem loop and 3′ hExo, a 3′–5′ exonuclease required for histone mRNA degradation, provided the first molecular insights into the architecture of this complex, and revealed how the hSLBP RBD forms a new RNA-binding motif to interact with the stem-loop RNA (18). On the other hand, how SLBP alone interacts with the RNA or how this interaction might be affected by phosphorylation of the TPNK motif is not known.Open in a separate windowFig. 1.Schematic of the domain architecture of dSLBP (Upper) and amino acid sequence alignment of RPDs of Drosophila and human SLBP (Lower). Domains of SLBP include the N-terminal domain (NTD), RBD, and C-terminal region (C). Amino acid sequences are shown with the RBD sequence in the top two rows and the C-terminal region in the bottom row. T230 in the TPNK motif and phosphorylation sites in the C-terminal region are indicated with boldface and asterisks, respectively; the residues involved in RNA binding are shown in cyan; and acidic residues in the C-terminal region are shown in red.The C-terminal region of dSLBP contains a motif, SNSDSDSD, whose hyperphosphorylation is required for efficient processing of histone pre-mRNA (15). Despite the similarity of hSLBP and dSLBP RBDs (55% identical residues) and their ability to bind identical stem-loop RNA sequences, neither SLBP can substitute for the other to process histone pre-mRNA in nuclear extracts; in fact, hSLBP inhibits processing of Drosophila histone pre-mRNA (15). This incompatibility results from differences in the C-terminal region (Fig. 1). The sequence C-terminal to the RBD in hSLBP is required for processing, but it is longer, has no similarity to the Drosophila sequence, and lacks phosphorylation sites.Here we focused on dSLBP and showed that phosphorylation greatly increases dSLBP binding affinity for the histone mRNA stem loop. Mimicking phosphorylation of the dSLBP RPD by mutation of phosphorylation sites to Glu residues at both the TPNK motif and the C-terminal region also boosted binding affinity relative to the nonphosphorylated dSLBP RPD. Structural studies of both the human and Drosophila SLBP RPD indicated that phosphorylation of the TPNK motif stabilizes the RNA-binding domain, but the C-terminal region is flexible in the protein:RNA complex and does not contact the RNA. Instead, we show that the increased negative charge in the C-terminal region of the dSLBP RPD results in a more compact ensemble of protein conformations in the absence of RNA, thereby increasing RNA-binding affinity by reducing the entropy of the unbound protein.