1H, 13C, and 15N chemical shift assignments for the N-terminal extracellular domain of T-cadherin.
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Cadherins↗
Biomedical subjects
Jörg Stetefeld
Publications and source records attributed to Jörg Stetefeld.
Activation of muscle-specific receptor tyrosine kinase and binding to dystroglycan are regulated by alternative mRNA splicing of agrin.
Agrin induces the aggregation of postsynaptic proteins at the neuromuscular junction (NMJ). This activity requires the receptor-tyrosine kinase MuSK. Agrin isoforms differ in short amino acid stretches at two sites, called A and B, that are localized in the two most C-terminal laminin G (LG) domains. Importantly, agrin isoforms greatly differ in their activities of inducing MuSK phosphorylation and of binding to alpha-dystroglycan. By using site-directed mutagenesis, we characterized the amino acids important for these activities of agrin. We find that the conserved tripeptide asparagineglutamate-isoleucine in the eight-amino acid long insert at the B-site is necessary and sufficient for full MuSK phosphorylation activity. However, even if all eight amino acids were replaced by alanines, this agrin mutant still has significantly higher MuSK phosphorylation activity than the splice version lacking any insert. We also show that binding to alpha-dystroglycan requires at least two LG domains and that amino acid inserts at the A and the B splice sites negatively affect binding.
Agrin↗
Tracking down the different forms of nuclear actin.
Actin is a rather uncommitted protein with a high degree of structural plasticity: it can adopt a variety of structural states, depending on the specific ionic conditions or the interaction with ligand proteins. These interactions lock actin into a distinct conformation, which specifies the oligomeric or polymeric form it can assume. The interplay between monomeric, oligomeric and polymeric forms is used by the cell to execute an enormous variety of motility processes, such as lamellipodium formation during locomotion or intracellular transport of vesicles. In these cytoplasmic events, monomeric G-actin and filamentous F-actin are the prevalent forms. However, there might be other structural states of actin in cells that have so far not received the attention they deserve. Here, we propose that specific, "unconventional" actin conformations might contribute especially to the multitude of functions executed by actin in the nucleus. We present evidence for the existence of different forms of nuclear actin, taken from studies with selected antibodies.
Actins↗
Structure/function analysis of spinalin, a spine protein of Hydra nematocysts.
The nematocyst capsules of the cnidarians are specialized explosive organelles that withstand high osmotic pressures of approximately 15 MPa (150 bar). A tight disulfide network involving cysteine-rich capsule wall proteins, like minicollagens and nematocyst outer wall antigen, characterizes their molecular composition. Nematocyst discharge leads to the expulsion of a long inverted tubule that was coiled inside the capsule matrix before activation. Spinalin has been characterized as a glycine-rich, histidine-rich protein associated with spine structures on the surface of everted tubules. Here, we show that full-length Hydra spinalin can be expressed recombinantly in HEK293 cells and has the property to form disulfide-linked oligomers, reflecting its state in mature capsules. Furthermore, spinalin showed a high tendency to associate into dimers in vitro and in vivo. Our data, which show incomplete disulfide connectivity in recombinant spinalin, suggest a possible mechanism by which the spine structure may be linked to the overall capsule polymer.
Animals↗
Ataxin-10 interacts with O-linked beta-N-acetylglucosamine transferase in the brain.
Modification by O-GlcNAc involves a growing number of eucaryotic nuclear and cytosolic proteins. Glycosylation of intracellular proteins is a dynamic process that in several cases competes with and acts as a reciprocal modification system to phosphorylation. O-Linked beta-N-acetylglucosamine transferase (OGT) levels are highest in the brain, and neurodegenerative disorders such as Alzheimer disease have been shown to involve abnormally phosphorylated key proteins, probably as a result of hypoglycosylation. Here, we show that the neurodegenerative disease protein ataxin-10 (Atx-10) is associated with cytoplasmic OGT p110 in the brain. In PC12 cells and pancreas, this association is competed by the shorter OGT p78 splice form, which is down-regulated in brain. Overexpression of Atx-10 in PC12 cells resulted in the reconstitution of the Atx-10-OGT p110 complex and enhanced intracellular glycosylation activity. Moreover, in an in vitro enzyme assay using PC12 cell extracts, Atx-10 increased OGT activity 2-fold. These data indicate that Atx-10 might be essential for the maintenance of a critical intracellular glycosylation level and homeostasis in the brain.
Acetylglucosamine↗
Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution.
Recombinant sorbitol dehydrogenase (SDH) from Rhodobacter sphaeroides has been crystallized in the absence of the cofactor NAD(H) and its structure determined to 2.4 A resolution using molecular replacement (refined R and R free factors of 18.8 and 23.8%, respectively). As expected from the sequence and shown by the conserved fold, SDH can be assigned to the short-chain dehydrogenase/reductase protein family. The cofactor NAD and the substrate sorbitol have been modelled into the structure and the active-site architecture, which displays the highly conserved catalytic tetrad of Asn-Ser-Tyr-Lys residues, is discussed in relation to the enzyme mechanism. This is the first structure of a bacterial SDH belonging to the SDR family.
Binding Sites↗
Favourable mediation of crystal contacts by cocoamidopropylbetaine (CAPB).
Crystals of excellent quality are a prerequisite for high-resolution X-ray data. However, in refinement protocols of crystallization conditions it is often difficult to obtain the right combination of, for example, protein concentration, drop size, temperature and additives. A novel approach for optimizing crystal contacts in a most favourable fashion by performing crystallization setups with the zwitterionic surfactant cocoamidoproylbetaine (CAPB) is introduced. In the presence of this surfactant, highly diffracting crystals were obtained. Here, data from a right-handed coiled coil (RHCC) in complex with CAPB at 1.4 A resolution are presented. The addition of CAPB using otherwise identical crystallization conditions and the same X-ray source caused an improvement in resolution from 2.9 to 1.4 A.
Archaeal Proteins↗
Structural and functional diversity generated by alternative mRNA splicing.
Alternative mRNA splicing is becoming increasingly recognized as an important mechanism for the generation of structural and functional diversity in proteins. Recent estimations predict that approximately 50% of all eukaryotic proteins can be alternatively spliced. Several lines of evidence suggest that alternative mRNA splicing results in small changes in protein structure and is likely to fine-tune the function and specificity of the affected protein. However, knowledge of how alternative splicing regulates cellular processes on the molecular level is still limited. It is only recently that structures of alternatively spliced proteins have been solved. These studies have shown that alternative splicing affects the structure not only in the vicinity of the splice site but also at long distance.
Alternative Splicing↗
Structure and laminin-binding specificity of the NtA domain expressed in eukaryotic cells.
Agrin is a key organizer for postsynaptic differentiation at the neuromuscular junction (NMJ). This activity requires the binding of agrin to the synaptic basal lamina via its N-terminal (NtA) domain. It has been suggested that this binding is mediated by conserved amino acids in the gamma 1 chain of laminin. Here, we report the crystal structure of chicken NtA expressed in eukaryotic HEK293 cells. In contrast to the previously published structure [Stetefeld, J., Jenny, M., Schulthess, T., Landwehr, R., Schumacher, B., Frank, S., Ruegg, M.A., Engel, J., Kammerer, R.A., 2001. The laminin-binding domain of agrin is structurally related to N-TIMP-1. Nat. Struct. Biol., 8, 705-709.], which was derived from the NtA domain expressed in E. coli, the new data show that the N-terminal tail region (amino acid residues Asn1-Arg5) is highly structured. Moreover, the disulfide bridge between Cys2 and Cys74 was also present. In addition, we show that the binding of NtA requires the gamma 1 chain of laminin and is not greatly affected by the composition of beta chains. These results confirm a model of the NtA-laminin complex where conserved amino acids in the gamma 1 chain are prerequisite for the binding to agrin and they further emphasize that the source of protein can be critical in structure determination.
Agrin↗
Design and crystal structure of bacteriophage T4 mini-fibritin NCCF.
Fibritin is a fibrous protein that forms "whiskers" attached to the neck of bacteriophage T4. Whiskers interact with the long tail fibers regulating the assembly and infectivity of the virus. The fibritin trimer includes the N-terminal domain responsible for attachment to the phage particle and for the collar formation, the central domain forming a 500 A long segmented coiled-coil structure, and the C-terminal "foldon" domain. We have designed a "mini" fibritin with most of the coiled-coil domain deleted, and solved its crystal structure. The non-helical N-terminal part represents a new protein fold that tightly interacts with the coiled-coil segment forming a single domain, as revealed by calorimetry. The analysis of the crystal structure and earlier electron microscopy data on the collar-whisker complex suggests the necessity of other proteins to participate in the collar formation. Crystal structure determination of the N-terminal domain of fibritin is the first step towards elucidating the detailed structure and assembly mechanism of the collar-whisker complex.
Amino Acid Motifs↗
Identification of functionally important residues in the pyridoxal-5'-phosphate-dependent catalytic antibody 15A9.
Antibody 15A9 is unique in its ability to catalyze the transamination reaction of hydrophobic D-amino acids with pyridoxal-5'-phosphate (PLP). Both previous chemical modification studies and a three dimensional (3-D) homology model indicated the presence of functionally important tyrosine residues in the antigen-binding cavity of antibody 15A9. To gain further insight into the hapten, ligand binding, and catalytic mechanism of 15A9, all tyrosine residues in the complementarity-determining regions (CDRs) and the single arginine residue in CDR3 of the light chain were subject to an alanine scan. Substitution of Tyr(H33), Tyr(L94), or Arg(L91) abolished the catalytic activity and reduced the affinity for PLP and N(a)-(5'-phosphopyridoxyl)-amino acids, which are close analogues of covalent PLP-substrate adducts. The Tyr(H100b)Ala mutant possessed no detectable catalytic activity, while its affinity for each ligand was essentially the same as that of the wild-type antibody. The binding affinity for the hapten was drastically reduced by a Tyr(L32)Ala mutation, suggesting that the hydroxyphenyl group of Tyr(L32) participates in the binding of the extended side chain of the hapten. The other Tyr --> Ala substitutions affected both binding and catalytic activity only to a minor degree. On the basis of the information obtained from the mutagenesis study, we docked N(alpha)-(5'-phosphopyridoxyl)-D-alanine into the antigen-binding site. According to this model, Arg(L91) binds the alpha-carboxylate group of the amino acid substrate and Tyr(H100b) plays an essential role in the catalytic mechanism of antibody 15A9 by facilitating the Calpha/C4' prototropic shift. In addition, the catalytic apparatus of antibody 15A9 revealed several mechanistic features that overlap with those of PLP-dependent enzymes.
Alanine↗
Proteolytic E-cadherin activation followed by solution NMR and X-ray crystallography.
Cellular adhesion by classical cadherins depends critically on the exact proteolytic removal of their N-terminal prosequences. In this combined solution NMR and X-ray crystallographic study, the consequences of propeptide cleavage of an epithelial cadherin construct (domains 1 and 2) were followed at atomic level. At low protein concentration, the N-terminal processing induces docking of the tryptophan-2 side-chain into a binding pocket on the same molecule. At high concentration, cleavage induces dimerization (KD=0.72 mM, k(off)=0.7 s(-1)) and concomitant intermolecular exchange of the betaA-strands and the tryptophan-2 side-chains. Thus, the cleavage represents the switch from a nonadhesive to the functional form of cadherin.
Amino Acid Sequence↗
Modulation of agrin function by alternative splicing and Ca2+ binding.
The aggregation of acetylcholine receptors on postsynaptic membranes is a key step in neuromuscular junction development. This process depends on alternatively spliced forms of the proteoglycan agrin with "B-inserts" of 8, 11, or 19 residues in the protein's globular C-terminal domain, G3. Structures of the neural B8 and B11 forms of agrin-G3 were determined by X-ray crystallography. The structure of G3-B0, which lacks inserts, was determined by NMR. The agrin-G3 domain adopts a beta jellyroll fold. The B insert site is flanked by four loops on one edge of the beta sandwich. The loops form a surface that corresponds to a versatile interaction interface in the family of structurally related LNS proteins. NMR and X-ray data indicate that this interaction interface is flexible in agrin-G3 and that flexibility is reduced by Ca(2+) binding. The plasticity of the interaction interface could enable different splice forms of agrin to select between multiple binding partners.
Agrin↗
Mapping of the laminin-binding site of the N-terminal agrin domain (NtA).
Agrin is a key organizer of acetylcholine receptor (AChR) clustering at the neuromuscular junction. The binding of agrin to laminin is required for its localization to synaptic basal lamina and other basement membranes. The high-affinity interaction with the coiled-coil domain of laminin is mediated by the N-terminal domain of agrin. We have adopted a structurally guided site-directed mutagenesis approach to map the laminin-binding site of NtA. Mutations of L117 and V124 in the C-terminal helix 3 showed that they are crucial for binding. Both residues are located in helix 3 and face the groove between the beta-barrel and the C-terminal helical segment of NtA. Remarkably, the distance between both residues matches a heptad repeat distance of two aliphatic residues which are solvent exposed in the coiled-coil domain of laminin. A lower but significant contribution originates from R43 and a charged cluster (E23, E24 and R40) at the open face of the beta-barrel structure. We propose that surface-exposed, conserved residues of the laminin gamma1 chain interact with NtA via hydrophobic and ionic interactions.
Agrin↗
Collagen stabilization at atomic level: crystal structure of designed (GlyProPro)10foldon.
In a designed fusion protein the trimeric domain foldon from bacteriophage T4 fibritin was connected to the C terminus of the collagen model peptide (GlyProPro)(10) by a short Gly-Ser linker to facilitate formation of the three-stranded collagen triple helix. Crystal structure analysis at 2.6 A resolution revealed conformational changes within the interface of both domains compared with the structure of the isolated molecules. A striking feature is an angle of 62.5 degrees between the symmetry axis of the foldon trimer and the axis of the triple helix. The melting temperature of (GlyProPro)(10) in the designed fusion protein (GlyProPro)(10)foldon is higher than that of isolated (GlyProPro)(10,) which suggests an entropic stabilization compensating for the destabilization at the interface.
Animals↗
Storage function of cartilage oligomeric matrix protein: the crystal structure of the coiled-coil domain in complex with vitamin D(3).
The five-stranded coiled-coil domain of cartilage oligomeric matrix protein (COMPcc) forms a continuous axial pore with binding capacities for hydrophobic compounds, including prominent cell signalling molecules. Here, we report the X-ray structure of the COMPcc domain in complex with vitamin D(3) at 1.7 A resolution. The COMPcc pentamer harbours two molecules of the steroid hormone precursor in a planar s-trans conformation of the conjugated triene, with the aliphatic tails lying along the molecule axis. A hydrophilic ring of five Gln54 side chains divides the channel into two hydrophobic compartments in which the bound vitamin D(3) pair is fixed in a head-to-head orientation. Vitamin D(3) binding induces a volumetric increase of the cavities of approximately 30% while the main chain distances of the pentamer are retained. This adaptation to the bulky ring systems of the ligands is accomplished by a rotamer re-orientation of beta-branched side chains that form the knobs into holes of the coiled-coil structure. Compared with binding of vitamin D and retinoic acid by their classical receptors, COMP exerts a distinct mechanism of interaction mainly defined by the pattern of hydrophobic core residues.
Animals↗
Pyridoxal-5'-phosphate-dependent catalytic antibodies.
Strategies for expanding the catalytic scope of antibodies include the incorporation of inorganic or organic cofactors into their binding sites. An obvious choice is pyridoxal-5'-phosphate (PLP), which is probably the most versatile organic cofactor of enzymes. Monoclonal antibodies against the hapten N(alpha)-(5'-phosphopyridoxyl)-L-lysine, a stable analog of the covalent coenzyme-substrate adducts were screened by a competition ELISA for binding of the PLP-amino acid Schiff base adduct. The Schiff base with its C4'-N alpha double bond is, in contrast to the hapten, a planar compound and is an obligatory intermediate in all PLP-dependent reactions of amino acids. This highly discriminating screening step eliminated all but 5 of 24 hapten-binding antibodies. The five remaining antibodies were tested for catalysis of the PLP-dependent alpha,beta-elimination reaction of beta-chloroalanine. Antibody 15A9 complied with this selection criterion and catalyzed in addition the cofactor-dependent transamination reaction of hydrophobic D-amino acids and oxo acids (k(cat)'=0.42 min(-1) with D-alanine at 25 degrees C). Homology modeling together with alanine scanning yielded a 3D model of Fab 15A9. The striking analogy between antibody 15A9 and PLP-dependent enzymes includes the following features: (1) The binding sites accommodate the planar coenzyme-amino acid adduct. (2) The bond at C alpha to be broken lies together with the C alpha-N bond in a plane orthogonal to the plane of coenzyme and imine bond. (3) The alpha-carboxylate group of the substrate is bound by an arginine residue. (4) The coenzyme-substrate adduct assumes a cisoid conformation. (5) PLP markedly contributes to catalytic efficiency, being a 10(4) times more efficient amino group acceptor than pyruvate. The protein moiety, however, ensures reaction as well as substrate specificity, and further accelerates the reaction (in 15A9 k(cat (Ab x PLP))'/k(cat (PLP))'=5 x 10(3)). The analogies of antibody 15A9 with PLP-dependent enzymes suggest that the selection criteria in the screening protocol were similar to those that have been operative in the molecular evolution of enzyme-assisted pyridoxal catalysis.
Amino Acids↗
Nucleation and propagation of the collagen triple helix in single-chain and trimerized peptides: transition from third to first order kinetics.
The kinetics of triple helix formation from single non-crosslinked peptide chains were studied for the collagen models (ProProGly)10 and (ProHypGly)10 in a broad concentration range and compared with those in nucleated trimers. At very low peptide concentrations the reaction order is 3 but decreases at higher concentrations. For (ProProGly)10 the third order rate constant is 800 M(-2) x s(-1) at 7 degrees C, which corresponds to a very long half time of 15 hours at 60 microM chain concentration. For (ProHypGly)10 the rate constant is about 1000-fold higher, which is consistent with the stabilizing effect of 4-hydroxyproline in collagens. The concentration dependence of the reaction order is explained by a nucleation mechanism in which a very unstable dimer is in fast equilibrium with the monomeric chains and addition of the third chain occurs in a rate-limiting step. At high concentrations nucleation is faster than propagation of helix formation and propagation becomes rate-limiting. To test this hypothesis an artificial nucleus was introduced by fusion of (ProProGly)10 with the trimeric foldon domain of T4 phage or the crosslinking domain of collagen III GlyProProGlyProCysCysGlyGlyGly. These domains were recombinantly attached to the C terminus of (GlyProPro)10 and link the three chains in a similar way to the C-terminal propeptide domain in collagen III. This results in a local intrinsic chain concentration of about 1 M. A first order reaction is observed for the folding of the triple helix in (GlyProPro)10foldon with a half time of 8.3 minutes, which approximately matches the rate of folding from single chains at 1 M peptide concentration. A high activation energy of 54 kJ/mol is found for this reaction, whereas the temperature dependence of the nucleation step is close to zero, confirming earlier findings on natural collagens that cis-trans isomerization of peptide bonds is the rate-limiting step in propagation.
Amino Acid Sequence↗