Keiko Kubota

Structural basis of abscisic acid signalling.

The phytohormone abscisic acid (ABA) mediates the adaptation of plants to environmental stresses such as drought and regulates developmental signals such as seed maturation. Within plants, the PYR/PYL/RCAR family of START proteins receives ABA to inhibit the phosphatase activity of the group-A protein phosphatases 2C (PP2Cs), which are major negative regulators in ABA signalling. Here we present the crystal structures of the ABA receptor PYL1 bound with (+)-ABA, and the complex formed by the further binding of (+)-ABA-bound PYL1 with the PP2C protein ABI1. PYL1 binds (+)-ABA using the START-protein-specific ligand-binding site, thereby forming a hydrophobic pocket on the surface of the closed lid. (+)-ABA-bound PYL1 tightly interacts with a PP2C domain of ABI1 by using the hydrophobic pocket to cover the active site of ABI1 like a plug. Our results reveal the structural basis of the mechanism of (+)-ABA-dependent inhibition of ABI1 by PYL1 in ABA signalling.

Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity

The tumor suppressor CYLD belongs to a ubiquitin (Ub)-specific protease (USP) family and specifically cleaves Met1- and Lys63-linked polyubiquitin chains to suppress inflammatory signaling pathways. Here, we report crystal structures representing the catalytic states of zebrafish CYLD for Met1- and Lys63-linked Ub chains and two distinct precatalytic states for Met1-linked chains. In both catalytic states, the distal Ub is bound to CYLD in a similar manner, and the scissile bond is located close to the catalytic residue, whereas the proximal Ub is bound in a manner specific to Met1- or Lys63-linked chains. Further structure-based mutagenesis experiments support the mechanism by which CYLD specifically cleaves both Met1- and Lys63-linked chains and provide insight into tumor-associated mutations of CYLD. This study provides new structural insight into the mechanisms by which USP family deubiquitinating enzymes recognize and cleave Ub chains with specific linkage types.

Molecular basis of Lys-63-linked polyubiquitination inhibition by the interaction between human deubiquitinating enzyme OTUB1 and ubiquitin-conjugating enzyme UBC13.

Background: A deubiquitinating enzyme OTUB1 inhibits Lys-63-linked ubiquitination by binding to a ubiquitin-conjugating enzyme UBC13. Results: A mechanism of human OTUB1-UBC13 interaction was revealed by human OTUB1-UBC13-MMS2 complex structure and structure-based mutagenesis. Conclusion: The atomic-level interactions presented by the OTUB1-UBC13-MMS2 complex structure are critical for Lys-63-linked ubiquitination inhibition. Significance: Learning how ubiquitination is regulated by the OTUB1-UBC13 interaction is crucial for understanding DNA damage response in biology. UBC13 is the only known E2 ubiquitin (Ub)-conjugating enzyme that produces Lys-63-linked Ub chain with its cofactor E2 variant UEV1a or MMS2. Lys-63-linked ubiquitination is crucial for recruitment of DNA repair and damage response molecules to sites of DNA double-strand breaks (DSBs). A deubiquitinating enzyme OTUB1 suppresses Lys-63-linked ubiquitination of chromatin surrounding DSBs by binding UBC13 to inhibit its E2 activity independently of the isopeptidase activity. OTUB1 strongly suppresses UBC13-dependent Lys-63-linked tri-Ub production, whereas it allows di-Ub production in vitro. The mechanism of this non-canonical OTUB1-mediated inhibition of ubiquitination remains to be elucidated. Furthermore, the atomic level information of the interaction between human OTUB1 and UBC13 has not been reported. Here, we determined the crystal structure of human OTUB1 in complex with human UBC13 and MMS2 at 3.15 Å resolution. The presented atomic-level interactions were confirmed by surface-plasmon resonance spectroscopy with structure-based mutagenesis. The designed OTUB1 mutants cannot inhibit Lys-63-linked Ub chain formation in vitro and histone ubiquitination and 53BP1 assembly around DSB sites in vivo. Finally, we propose a model for how capping of di-Ub by the OTUB1-UBC13-MMS2/UEV1a complex efficiently inhibits Lys-63-linked tri-Ub formation.

Crystal Structure of γ-Hexachlorocyclohexane Dehydrochlorinase LinA from Sphingobium japonicum UT26

LinA from Sphingobium japonicum UT26 catalyzes two steps of dehydrochlorination from γ hexachlorocyclohexane (HCH) to 1,3,4,6-tetrachloro-1,4-cyclohexadiene via γ-pentachlorocyclohexene. We determined the crystal structure of LinA at 2.25 Å by single anomalous dispersion. LinA exists as a homotrimer, and each protomer forms a cone-shaped α+β barrel fold. The C-terminal region of LinA is extended to the neighboring subunit, unlike that of scytalone dehydratase from Magnaporthe grisea, which is one of the most structurally similar proteins identified by the DALI server. The structure we obtained in this study is in open form, in which γ-HCH can enter the active site. There is a hydrophobic cavity inside the barrel fold, and the active site is largely surrounded by the side chains of K20, L21, V24, D25, W42, L64, F68, C71, H73, V94, L96, I109, F113, and R129. H73 was considered to function as a base that abstracts the proton of γ-HCH through its interaction with D25. Docking simulations with γ-HCH and γ-pentachlorocyclohexene suggest that 11 residues (K20, I44, L64, V94, L96, I109, A111, F113, A131, C132, and T133) are involved in the binding of these compounds and support the degradation mechanism.

Identification of a glutamine residue essential for catalytic activity of aspergilloglutamic peptidase by site-directed mutagenesis

Aspergilloglutamic peptidase (AGP, formerly called aspergillopepsin II) from Aspergillus niger var. macrosporus is a unique acid protease recently classified to the peptidase family G1. Our previous study using site‐directed mutagenesis on the glutamic and aspartic acid residues of AGP conserved among the G1 family suggested that Glu219 and Asp123 (numbering in the preproform) are important for catalytic activity. However, the Asn mutant of Asp123 retained weak but significant activity and therefore it was unclear whether it is an active site residue. In this study, we performed site‐directed mutagenesis on all the other hydrophilic residues including Gln, Asn, Ser, Thr, and Tyr, conserved in this family to screen other residues that might be essential for catalytic function, and found that mutations of only Gln133 resulted in almost complete loss of enzymatic activity without change in the native conformation of the enzyme. Meanwhile, the 3D structure of scytalidoglutamic peptidase, a homologue from Scytalidium lignicolum, has been reported, indicating that Glu136 and Gln53 (the counterparts of Glu219 and Gln133 in AGP) form a catalytic dyad. Therefore, the results obtained in this and our previous studies provide with complementary evidence for the definitive conclusion on the catalytic function of the Glu/Gln dyad in glutamic peptidases.

Get1 Stabilizes an Open Dimer Conformation of Get3 ATPase by Binding Two Distinct Interfaces

Tail-anchored (TA) proteins are integral membrane proteins that possess a single transmembrane domain near their carboxy terminus. TA proteins play critical roles in many important cellular processes such as membrane trafficking, protein translocation, and apoptosis. The GET complex mediates posttranslational insertion of newly synthesized TA proteins to the endoplasmic reticulum membrane. The GET complex is composed of the homodimeric Get3 ATPase and its heterooligomeric receptor, Get1/2. During insertion, the Get3 dimer shuttles between open and closed conformational states, coupled with ATP hydrolysis and the binding/release of TA proteins. We report crystal structures of ADP-bound Get3 in complex with the cytoplasmic domain of Get1 (Get1CD) in open and semi-open conformations at 3.0- and 4.5-Å resolutions, respectively. Our structures and biochemical data suggest that Get1 uses two interfaces to stabilize the open dimer conformation of Get3. We propose that one interface is sufficient for binding of Get1 by Get3, while the second interface stabilizes the open dimer conformation of Get3.

Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3

Circadian rhythms, biological oscillations of physiological activities with a period of 24 h, are found in a wide spectrum of organisms and enhance their fitness in a day/night cycle. The simplest cells that are known to exhibit circadian rhythms are prokaryotic cyanobacteria,1 where considerable progress has been recently achieved in the identification of essential clock proteins and their structures. Circadian rhythm is controlled by a cluster of three genes: kaiA, kaiB, and kaiC.2 Among these genes, KaiC is a crucial protein, forming a stable homohexamer upon binding of ATP. The KaiC has a double-domain structure of the N-terminal domain (KaiCI) and the Cterminal domain (KaiCII).3 KaiCI is responsible for the ATP induced hexamerizaion of KaiC, while the KaiCII is flexible and responsible for the phosphorylation of KaiC.3 The autophosphorylation of KaiC is stimulated by KaiA, whereas KaiB antagonizes the effects of KaiA on KaiC autophosphorylation.4 Recently, KaiC homologues have been found in almost all species of archaea such as Pyrococcus and Sulfolobus.5 Most of the KaiC homologues in archaea are short (single-domain) versions different from those of cyanobacteria. The function of kaiC homologues genes in archaea remains unknown. Pyrococcus horikoshii OT3 has homologous proteins of the KaiC-domain, PH0186 and PH0187, which seem to form the operon on the genome similar to the double-domain architecture of cyanobacterial KaiC. The amino acid sequence of PH0186 shares 35% identity with that of KaiCI whose structure has already been determined and contains a Walker A motif, a Walker B motif, and catalytic Glu residues,6 which are also found in KaiCI. To elucidate the structure and function of the KaiC homologous proteins in archaea, we determined the first structure of PH0186 by X-ray crystallography at 2.07 Å resolution by the multiwavelength anomalous dispersion (MAD) method.

Specific Inhibition and Stabilization of Aspergilloglutamic Peptidase by the Propeptide IDENTIFICATION OF CRITICAL SEQUENCES AND RESIDUES IN THE PROPEPTIDE

Aspergilloglutamic peptidase (formerly called aspergillopepsin II) is an acid endopeptidase produced by Aspergillus niger var. macrosporus, with a novel catalytic dyad of a glutamic acid and a glutamine residue, thus belonging to a novel peptidase family G1. The mature enzyme is generated from its precursor by removal of the putative 41-residue propeptide and an 11-residue intervening peptide through autocatalytic activation. In the present study, the propeptide (Ala1–Asn41) and a series of its truncated peptides were chemically synthesized, and their effects on the enzyme activity and thermal stability were examined to identify the sequences and residues in the propeptide most critical to the inhibition and thermal stabilization. The synthetic propeptide was shown to be a potent competitive inhibitor of the enzyme (Ki = 27 nm at pH 4.0). Various shorter propeptide fragments derived from the central region of the propeptide had significant inhibitory effect, whereas their Ala scan-substituted peptides, especially R19A and H20A, showed only weak inhibition. Substitution of the Pro23-Pro24 sequence near His20 with an Ala-Ala sequence changed the peptide Lys18–Tyr25 to a substrate with His20 as the P1 residue. Furthermore, the propeptide was shown to be able to significantly protect the enzyme from thermal denaturation (ΔTm = ∼19 °C at pH 5.6). The protective potencies of the propeptide as well as truncated propeptides and their Ala scan-substituted peptides are parallel with their inhibitory potencies. These results indicate that the central part, and especially Arg19 and His20 therein, of the propeptide is most critical to the inhibition and thermal stabilization and that His20 interacts with the enzyme at or near the S1 site in a nonproductive fashion.

Crystallization and preliminary X-ray analysis of ZHE1, a hatching enzyme from the zebrafish Danio rerio.

The hatching enzyme of the zebrafish, ZHE1 (29.3 kDa), is a zinc metalloprotease that catalyzes digestion of the egg envelope (chorion). ZHE1 was heterologously expressed in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant. Two diffraction data sets with resolution ranges 50.0-1.80 and 50.0-1.14 A were independently collected from two crystals and were merged to give a highly complete data set over the full resolution range 50.0-1.14 A. The space group was assigned as primitive orthorhombic P2(1)2(1)2(1), with unit-cell parameters a = 32.9, b = 62.5, c = 87.4 A. The crystal contained one ZHE1 molecule in the asymmetric unit.

Crystallization and preliminary X-ray analysis of γ-­hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26

LinA from Sphingobium japonicum UT26 catalyzes two steps of dehydrochlorination from gamma-hexachlorocyclohexane (gamma-HCH) to 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN) via gamma-pentachlorocyclohexene (gamma-PCCH). LinA was crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as the precipitant. The crystals belonged to space group P4(1) or P4(3), with unit-cell parameters a = b = 68.9, c = 101.9 A, and diffracted X-rays to 2.25 A resolution. The crystal contained three molecules in the asymmetric unit.