Alexander Zdanov

Crystal structure of plant aspartic proteinase prophytepsin: inactivation and vacuolar targeting

We determined at 2.3 Å resolution the crystal structure of prophytepsin, a zymogen of a barley vacuolar aspartic proteinase. In addition to the classical pepsin‐like bilobal main body of phytepsin, we also traced most of the propeptide, as well as an independent plant‐specific domain, never before described in structural terms. The structure revealed that, in addition to the propeptide, 13 N‐terminal residues of the mature phytepsin are essential for inactivation of the enzyme. Comparison of the plant‐specific domain with NK‐lysin indicates that these two saposin‐like structures are closely related, suggesting that all saposins and saposin‐like domains share a common topology. Structural analysis of prophytepsin led to the identification of a putative membrane receptor‐binding site involved in Golgi‐mediated transport to vacuoles.

Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase

Porphobilinogen synthase (PBGS) catalyzes the first common step in the biosynthesis of tetrapyrroles (such as heme and chlorophyll). Although the predominant oligomeric form of this enzyme, as inferred from many crystal structures, is that of a homo-octamer, a rare human PBGS allele, F12L, reveals the presence of a hexameric form. Rearrangement of an N-terminal arm is responsible for this oligomeric switch, which results in profound changes in kinetic behavior. The structural transition between octamer and hexamer must proceed through an unparalleled equilibrium containing two different dimer structures. The allosteric magnesium, present in most PBGS, has a binding site in the octamer but not in the hexamer. The unprecedented structural rearrangement reported here relates to the allosteric regulation of PBGS and suggests that alternative PBGS oligomers may function in a magnesium-dependent regulation of tetrapyrrole biosynthesis in plants and some bacteria.

Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction.

The crystal structure of the cyclic phosphodiesterase (CPDase) from Arabidopsis thaliana, an enzyme involved in the tRNA splicing pathway, was determined at 2.5 Å resolution. CPDase hydrolyzes ADP‐ribose 1″,2″‐cyclic phosphate (Appr>p), a product of the tRNA splicing reaction, to the monoester ADP‐ribose 1″‐phosphate (Appr‐1″p). The 181 amino acid protein shows a novel, bilobal arrangement of two αβ modules. Each lobe consists of two α‐helices on the outer side of the molecule, framing a three‐ or four‐stranded antiparallel β‐sheet in the core of the protein. The active site is formed at the interface of the two β‐sheets in a water‐filled cavity involving residues from two H‐X‐T/S‐X motifs. This previously noticed motif participates in coordination of a sulfate ion. A solvent‐exposed surface loop (residues 100–115) is very likely to play a flap‐like role, opening and closing the active site. Based on the crystal structure and on recent mutagenesis studies of a homologous CPDase from Saccharomyces cerevisiae, we propose an enzymatic mechanism that employs the nucleophilic attack of a water molecule activated by one of the active site histidines.

Crystal structure of human interferon-λ1 in complex with its high-affinity receptor interferon-λR1.

Abstract Interferon (IFN)-λ1 [also known as interleukin (IL)-29] belongs to the recently discovered group of type III IFNs. All type III IFNs initiate signaling processes through formation of specific heterodimeric receptor complexes consisting of IFN-λR1 and IL-10R2. We have determined the structure of human IFN-λ1 complexed with human IFN-λR1, a receptor unique to type III IFNs. The overall structure of IFN-λ1 is topologically similar to the structure of IL-10 and other members of the IL-10 family of cytokines. IFN-λR1 consists of two distinct domains having fibronectin type III topology. The ligand–receptor interface includes helix A, loop AB, and helix F on the IFN site, as well as loops primarily from the N-terminal domain and inter-domain hinge region of IFN-λR1. Composition and architecture of the interface that includes only a few direct hydrogen bonds support an idea that long-range ionic interactions between ligand and receptor govern the process of initial recognition of the molecules while hydrophobic interactions finalize it.

Structure and Mechanism of the Saposin-like Domain of a Plant Aspartic Protease

Many plant aspartic proteases contain an additional sequence of ∼100 amino acids termed the plant-specific insert, which is involved in host defense and vacuolar targeting. Similar to all saposin-like proteins, the plant-specific insert functions via protein-membrane interactions; however, the structural basis for such interactions has not been studied, and the nature of plant-specific insert-mediated membrane disruption has not been characterized. In the present study, the crystal structure of the saposin-like domain of potato aspartic protease was resolved at a resolution of 1.9 Å, revealing an open V-shaped configuration similar to the open structure of human saposin C. Notably, vesicle disruption activity followed Michaelis-Menten-like kinetics, a finding not previously reported for saposin-like proteins including plant-specific inserts. Circular dichroism data suggested that secondary structure was pH-dependent in a fashion similar to influenza A hemagglutinin fusion peptide. Membrane effects characterized by atomic force microscopy and light scattering indicated bilayer solubilization as well as fusogenic activity. Taken together, the present study is the first report to elucidate the membrane interaction mechanism of plant saposin-like domains whereby pH-dependent membrane interactions resulted in bilayer fusogenic activity that probably arose from a viral type pH-dependent helix-kink-helix motif at the plant-specific insert N terminus.

A model of the ternary complex of interleukin-10 with its soluble receptors

BackgroundInterleukin-10 (IL-10) is a cytokine whose main biological function is to suppress the immune response by induction of a signal(s) leading to inhibition of synthesis of a number of cytokines and their cellular receptors. Signal transduction is initiated upon formation of a ternary complex of IL-10 with two of its receptor chains, IL-10R1 and IL-10R2, expressed on the cell membrane. The affinity of IL-10R1 toward IL-10 is very high, which allowed determination of the crystal structure of IL-10 complexed with the extracellular/soluble domain of IL-10R1, while the affinity of IL-10R2 toward either IL-10 or IL-10/sIL-10R1 complex is quite low. This so far has prevented any attempts to obtain structural information about the ternary complex of IL-10 with its receptor chains.ResultsStructures of the second soluble receptor chain of interleukin-10 (sIL-10R2) and the ternary complex of IL-10/sIL-10R1/sIL-10R2 have been generated by homology modeling, which allowed us to identify residues involved in ligand-receptor and receptor-receptor interactions.ConclusionThe previously experimentally determined structure of the intermediate/binary complex IL-10/sIL-10R1 is the same in the ternary complex. There are two binding sites for the second receptor chain on the surface of the IL-10/sIL-10R1 complex, involving both IL-10 and sIL-10R1. Most of the interactions are hydrophilic in nature, although each interface includes two internal hydrophobic clusters. The distance between C-termini of the receptor chains is 25 Å, which is common for known structures of ternary complexes of other cytokines. The structure is likely to represent the biologically active signaling complex of IL-10 with its receptor on the surface of the cell membrane.

Stoichiometry of the complex of human interleukin‐4 with its receptor

A large number of cytokines have been shown to possess a four‐helix bundle structure with a unique up‐up‐down‐down connectivity. The receptors for this family of cytokines have been shown to be homologous as well, each possessing two tandem repeats of a fibronectin type III‐like domain. The crystal structure of human growth hormone bound to the soluble portion of its receptor has served as the only experimentally‐determined example of the interaction between the four‐helix bundle cytokines and their receptors: Two identical receptor subunits bind to different epitopes on the same growth hormone ligand. We have conducted a series of experiments to determine if this structural paradigm is true for interleukin‐4 and interleukin‐4 receptor. Native polyacrylamide gel electrophoresis and gel filtration chromatography reveal that interleukin‐4 forms a tight 1:1 complex with the soluble portion of interleukin‐4 receptor and is thus unlike the growth hormone system.

A New Look at Cytokine Signaling

Signal transduction is initiated when a cytokine binds to the extracellular domains of its receptors, bringing them together and triggering a complicated sequence of events inside the cell. In this issue, LaPorte et al. (2008) present crystal structures of three signaling complexes of the cytokines interleukin-4 and interleukin-13 with their receptors, showing how events taking place outside the cell may affect the specificity of signal transduction.

Purification, crystallization and preliminary crystallographic studies of the complex of interferon-λ1 with its receptor

Human interferon-lambda1 (IFN-lambda1(Ins)) and the extracellular domain of interferon-lambda1 receptor (IFN-lambda1R1) were expressed in Drosophila S2 cells and purified to homogeneity. Both IFN-lambda1(Ins) and interferon-lambda1 produced from Escherichia coli (IFN-lambda1(Bac)) were coupled with IFN-lambda1R1 at room temperature and the complexes were purified by gel filtration. Both complexes were crystallized; the crystals were flash-frozen at 100 K and diffraction data were collected to 2.16 and 2.1 A, respectively. Although the IFN-lambda1(Bac)-IFN-lambda1R1 and IFN-lambda1(Ins)-IFN-lambda1R1 complexes differed only in the nature of the expression system used for the ligand, their crystallization conditions and crystal forms were quite different. A search for heavy-atom derivatives as well as molecular-replacement trials are in progress.

Crystal structure of the complex of human interferon-λ1 with its high affinity receptor interferon-λR1

Abstract Interferon (IFN)-λ1 [also known as interleukin (IL)-29] belongs to the recently discovered group of type III IFNs. All type III IFNs initiate signaling processes through formation of specific heterodimeric receptor complexes consisting of IFN-λR1 and IL-10R2. We have determined the structure of human IFN-λ1 complexed with human IFN-λR1, a receptor unique to type III IFNs. The overall structure of IFN-λ1 is topologically similar to the structure of IL-10 and other members of the IL-10 family of cytokines. IFN-λR1 consists of two distinct domains having fibronectin type III topology. The ligand–receptor interface includes helix A, loop AB, and helix F on the IFN site, as well as loops primarily from the N-terminal domain and inter-domain hinge region of IFN-λR1. Composition and architecture of the interface that includes only a few direct hydrogen bonds support an idea that long-range ionic interactions between ligand and receptor govern the process of initial recognition of the molecules while hydrophobic interactions finalize it.