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Yoshiki Yamaguchi

Publications and source records attributed to Yoshiki Yamaguchi.

At least 19 recordsLinked to original sources
PubMed2007

Direct interactions between NEDD8 and ubiquitin E2 conjugating enzymes upregulate cullin-based E3 ligase activity.

Although cullin-1 neddylation is crucial for the activation of SCF ubiquitin E3 ligases, the underlying mechanisms for NEDD8-mediated activation of SCF remain unclear. Here we demonstrate by NMR and mutational studies that NEDD8 binds the ubiquitin E2 (UBC4), but not NEDD8 E2 (UBC12). Our data imply that NEDD8 forms an active platform on the SCF complex for selective recruitment of ubiquitin-charged E2s in collaboration with RBX1, and thereby upregulates the E3 activity.

Carrier Proteins↗
PubMed2006

Hydrogen bonding makes a difference in the rhodium-catalyzed enantioselective hydrogenation using monodentate phosphoramidites.

A new generation of monodentate phosphoramidite ligands bearing a primary amine moiety was found to display comparable or better efficiency than bisphosphines in the Rh-catalyzed asymmetric hydrogenation of challenging substrates, such as (Z)-methyl alpha-acetoxyacrylate or (E)-beta-aryl itaconate derivatives, affording the corresponding hydrogenation products with excellent enantioselectivities (up to >99% ee). The presence of intermolecular hydrogen bonding (HB) between two monodentate ligands in the catalyst was found to be critical for excellent catalyst performance. This finding provides a basis for design and development of further catalyst systems using this type of monodentate phosphoramidite ligands.

Catalysis↗
PubMed2006

Evolutionally conserved intermediates between ubiquitin and NEDD8.

The investigation of common structural motifs provides additional information on why proteins conserve similar topologies yet may have non-conserved amino acid sequences. Proteins containing the ubiquitin superfold have similar topologies, although the sequence conservation is rather poor. Here, we present novel similarities and differences between the proteins ubiquitin and NEDD8. They have 57% identical sequence, almost identical backbone topology and similar functional strategy, although their physiological functions are mutually different. Using variable pressure NMR spectroscopy, we found that the two proteins have similar conformational fluctuation in the evolutionary conserved enzyme-binding region and contain a structurally similar locally disordered conformer (I) in equilibrium with the basic folded conformer (N). A notable difference between the two proteins is that the equilibrium population of I is far greater for NEDD8 (DeltaG(0)(NI)<5 kJ/mol) than for ubiquitin (DeltaG(0)(NI)=15.2(+/-1.0) kJ/mol), and that the tendency for overall unfolding (U) is also far higher for NEDD8 (DeltaG(0)(NU)=11.0(+/-1.5) kJ/mol) than for ubiquitin (DeltaG(0)(NU)=31.3(+/-4.7) kJ/mol). These results suggest that the marked differences in thermodynamic stabilities of the locally disordered conformer (I) and the overall unfolding species (U) are a key to determine the functional differences of the two structurally similar proteins in physiology.

Amino Acid Sequence↗
PubMed2006

Peptide recognition: encapsulation and alpha-helical folding of a nine-residue peptide within a hydrophobic dimeric capsule of a bowl-shaped host.

A dimeric capsule of coordination bowl 1 encapsulated a nine-residue peptide (Trp-Ala-Glu-Ala-Ala-Ala-Glu-Ala-Trp; 2) within the large hydrophobic cavity in water, and stabilized the alpha-helical conformation of bound 2. An NMR titration experiment revealed that monomeric bowl 1 recognized two Trp residues at the both terminals of 2 through 1/2 = 1:1 to 2:1 complexation. The 1:1 and 2:1 species exist in equilibrium even in the presence of excess 1. It was found that the formation of the 2:1 complex, in which two bowls of 1 wrapped the whole of 2, became dominant by the addition of NaNO3 due to the fact that the enhanced ion strength increased the hydrophobic interaction between Trp residues and the cavity of 1. The alpha-helical conformation of 2 within the dimeric capsule of 1 was elucidated from detailed NOESY analysis.

Dimerization↗
PubMed2006

Solution structure and dynamics of Ufm1, a ubiquitin-fold modifier 1.

The ubiquitin-fold modifier 1 (Ufm1) is one of various ubiquitin-like modifiers and conjugates to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting its potential roles in various multicellular organisms. Herein, we analyzed the solution structure and dynamics of human Ufm1 (hsUfm1) by nuclear magnetic resonance spectroscopy. Although the global fold of hsUfm1 is similar to those of ubiquitin (Ub) and NEDD8, the cluster of acidic residues conserved in Ub and NEDD8 does not exist on the Ufm1 surface. 15N spin relaxation data revealed that the amino acid residues of hsUfm1 exhibiting conformational fluctuations form a cluster at the C-terminal segment and its spatial proximity, which correspond to the versatile ligand-binding sites of Ub and other ubiquitin-like proteins (Ubls). We suggest that Ub and other Ubl-modifiers share a common feature of potential conformational multiplicity, which might be associated with the broad ligand specificities of these proteins.

Amino Acid Sequence↗
PubMed2006

Solution structures and behavior of trans-RuH(eta(1)-BH(4)) (binap)(1,2-diamine) complexes.

The solution structures of a number of trans-RuH(eta(1)-BH(4))[(S)-tolbinap](1,2-diamine) precatalysts [TolBINAP = 2,2'-bis(di-4-tolylphosphino)-1,1'-binaphthyl; 1,2-diamine==(S,S)- or (R,R)-1,2-diphenylethylenediamine (DPEN), ethylenediamine (EN), and (S)-1,1-di(4-anisyl)-2-isopropylethylenediamine (DAIPEN)] have been determined using 2D NMR ((1)H--(1)H DQF-COSY, (1)H--(13)C HMQC, (1)H--(31)P HSQC, and (1)H--(15)N HSQC), and a double-pulsed field-gradient spin-echo (DPFGSE) NOE technique. All the octahedral Ru complexes adopt a trans configuration with respect to the BH(4) and hydride ligands. Amine protons of trans-RuH(eta(1)-BH(4))[(S)-tolbinap](1,2-diamine) complexes undergo H/D exchange in (CD(3))(2)CDOD. This inherent high acidity, coupled with the lability and chemical properties of the BH(4) ligand, allows for precatalyst activation without the need for an added base, in contrast to trans-RuCl(2)[(S)-tolbinap](1,2-diamine) precatalysts, which require a strong base for generation of a catalytic species. The H/BH(4) complex in a 2-propanol solution is converted to catalytically active [trans-RuH{(S)-tolbinap}{(S,S)-dpen}(ROH)](+) [(RO)(ROH)(n)](-) (R = (CH(3))(2)CH), a loosely associated ion pair of the discrete (solvated) cationic fragment and anionic species.

Amines↗
PubMed2005

Glycoform-dependent conformational alteration of the Fc region of human immunoglobulin G1 as revealed by NMR spectroscopy.

The Fc portion of immunoglobulin G (IgG) expresses the biantennary complex type oligosaccharides at Asn297 of the C(H)2 domain of each heavy chain with microheterogeneities depending on physiological and pathological states. These N-glycans are known to be essential for promotion of proper effector functions of IgG such as complement activation and Fcgamma receptor (FcgammaR)-mediated activities. To gain a better understanding of the role of Fc glycosylation, we prepared a series of truncated glycoforms of human IgG1-Fc and analyzed their interactions with human soluble FcgammaRIIIa (sFcgammaRIIIa) and with staphylococcal protein A by surface plasmon resonance and nuclear magnetic resonance (NMR) methods. Progressive but less pronounced reductions in the affinity for sFcgammaRIIIa were observed as a result of the galactosidase and subsequent N-acetylhexosaminidase treatments of IgG1-Fc. The following endoglycosidase D treatment, giving rise to a disaccharide structure composed of a fucosylated GlcNAc, abrogated the affinity of IgG1-Fc for sFcgammaRIIIa. On the other hand, those glycosidase treatments did not significantly affect the affinity of IgG1-Fc for protein A. Inspection of stable-isotope-assisted NMR data of a series of Fc glycoforms indicates that the stepwise trimming out of the carbohydrate residues results in concomitant increase in the number of amino acid residues perturbed thereby in the C(H)2 domains. Furthermore, the cleavage at the GlcNAcbeta1-4GlcNAc glycosidic linkage induced the conformational alterations of part of the lower hinge region, which makes no direct contact with the carbohydrate moieties and forms the major FcgammaR-binding site, while the conformation of the C(H)2/C(H)3 interface was barely perturbed that is the protein A-binding site. These results indicate that the carbohydrate moieties are required for maintaining the structural integrity of the FcgammaR-binding site.

Binding Sites↗
PubMed2005

Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.

Tom1 (Target of Myb1) is suggested to be involved in the transport of ubiquitinated proteins, through the interaction of its GAT (GGA and Tom1) domain with ubiquitin. Here, we demonstrate that the three-helix bundle of Tom1-GAT has two ubiquitin-binding sites recognizing the hydrophobic Ile44 surface of ubiquitin. The complex crystal structure demonstrates that the first site is a hydrophobic patch on helices alpha1 and alpha2. NMR and biochemical data revealed that the N-terminal half of helix alpha3 of Tom1-GAT constitutes the second, stronger binding site. The double-sided ubiquitin binding enhances the efficiency of recognition of ubiquitinated proteins by Tom1.

Amino Acid Sequence↗
PubMed2005

Sugar-binding properties of VIP36, an intracellular animal lectin operating as a cargo receptor.

The vesicular integral protein of 36 kDa (VIP36) is an intracellular animal lectin that acts as a putative cargo receptor, which recycles between the Golgi and the endoplasmic reticulum. Although it is known that VIP36 interacts with glycoproteins carrying high mannose-type oligosaccharides, detailed analyses of the sugar-binding specificity that discriminates isomeric oligosaccharide structures have not yet been performed. In the present study, we have analyzed, using the frontal affinity chromatography (FAC) method, the sugar-binding properties of a recombinant carbohydrate recognition domain of VIP36 (VIP36-CRD). For this purpose, a pyridylaminated sugar library, consisting of 21 kinds of oligosaccharides, including isomeric structures, was prepared and subjected to FAC analyses. The FAC data have shown that glucosylation and trimming of the D1 mannosyl branch interfere with the binding of VIP36-CRD. VIP36-CRD exhibits a bell-shaped pH dependence of sugar binding with an optimal pH value of approximately 6.5. By inspection of the specificity and optimal pH value of the sugar binding of VIP36 and its subcellular localization, together with the organellar pH, we suggest that VIP36 binds glycoproteins that retain the intact D1 mannosyl branch in the cis-Golgi network and recycles to the endoplasmic reticulum where, due to higher pH, it releases its cargos, thereby contributing to the quality control of glycoproteins.

Chromatography, Affinity↗
PubMed2005

Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten.

Antigen-induced structural changes in the Fv fragment of an anti-dansyl immunoglobulin G were studied by X-ray crystallography and stopped-flow fluorescence measurement. The crystal structure of the Fv fragment complexed with dansyl-lysine was determined at a resolution of 1.85 A. The dansyl-lysine molecule bound to a narrow cavity formed by the complementarity-determining regions H3 and H1, the N-terminal region of the VH domain and L2 of the VL domain. The structure of the binding site in the crystal structure explained well the results of the previous nuclear magnetic resonance measurements. The hapten binding caused remarkable conformational changes in H3 and its environmental structures, including the hydration structure from those observed in the unliganded state. The tip of H3 moved about 12 A from its position in the unliganded state. In addition, because of the contacts of H3 with the VL domain at the domain interface, the conformational changes of H3 resulted in the relative rotation of the variable domains by 5 degrees from their association observed in the unliganded state. The hydrophobic interactions at the domain interface seemed to be particularly important for the mutual rotation of the domains. The stopped-flow fluorescence measurement monitoring the interaction of the dansyl group and the binding pocket revealed that H3 was in a conformational equilibrium of three consecutive conformational states in the presence of dansyl-lysine in solution; an unliganded state preventing the access of the hapten, another unliganded state able to bind the hapten and the complex. The conformational dynamics of H3 in recognizing and binding the hapten molecule are discussed on the basis of the structural information from the present and previous studies.

Binding Sites↗
PubMed2005

Development of structural analysis of sulfated N-glycans by multidimensional high performance liquid chromatography mapping methods.

Although the biological importance of sulfated oligosaccharides has been widely recognized, there are only a few reports that describe detailed structures of sulfated N-glycans. This is largely due to the lack of a convenient method to identify structures of sulfated glycans found in low incidence. Here we develop multidimensional high performance liquid chromatography (HPLC) mapping methods for rapid and convenient identification of sulfated N-glycans. By using adequate quantities of sulfated N-glycans derived from LS12 cells, which are transfected with sulfotransferase cDNA, 40 different sulfated glycans have been successfully mapped. Furthermore, we have applied the HPLC data to identification of isomeric products resulting from an enzymatic reaction of N-acetylglucosamine 6-O-sulfotransferase-1 in vitro and revealed that this enzyme preferentially catalyzes sulfation of the GlcNAcbeta1-->2Manalpha1-->3Man branch in a biantennary acceptor.

Animals↗
PubMed2005

Molecular mechanism of ubiquitin recognition by GGA3 GAT domain.

GGA (Golgi-localizing, gamma-adaptin ear domain homology, ARF-binding) proteins, which constitute a family of clathrin coat adaptor proteins, have recently been shown to be involved in the ubiquitin-dependent sorting of receptors, through the interaction between the C-terminal three-helix-bundle of the GAT (GGA and Tom1) domain (C-GAT) and ubiquitin. We report here the crystal structure of human GGA3 C-GAT in complex with ubiquitin. A hydrophobic patch on C-GAT helices alpha1 and alpha2 forms a binding site for the hydrophobic Ile44 surface of ubiquitin. Two distinct orientations of ubiquitin Arg42 determine the shape and the charge distribution of ubiquitin Ile44 surface, leading to two different binding modes. Biochemical and NMR data strongly suggest another hydrophobic binding site on C-GAT helices alpha2 and alpha3, opposite to the first binding site, also binds ubiquitin although weakly. The double-sided ubiquitin binding provides the GAT domain with higher efficiency in recognizing ubiquitinated receptors for lysosomal receptor degradation.

ADP-Ribosylation Factors↗
PubMed2004

Gentamicin binds to the lectin site of calreticulin and inhibits its chaperone activity.

Recently, it became clear that aminoglycoside antibiotics affect protein-protein interactions involving protein disulfide isomerase as well as protein synthesis in the endoplasmic reticulum. In this study, we used affinity column chromatography to screen gentamicin-binding proteins in microsomes derived from bovine kidney in order to learn about the possible mechanisms of gentamicin-associated nephrotoxicity. One of the gentamicin-binding proteins was identified as calreticulin (CRT) by N-terminal amino acid sequence analysis. Interestingly, gentamicin inhibited the chaperone and oxidative refolding activities of CRT when N-glycosylated substrates such as alpha1-antitrypsin and alpha-mannosidase were used as substrates, but it did not inhibit the chaperone activity of CRT when unglycosylated citrate synthase was used. Moreover, CRT suppressed the aggregation of deglycosylated and denatured alpha-mannosidase, but gentamicin did not inhibit its chaperone activity. Experiments with domain mutants suggest that the lectin site of CRT is the main target for gentamicin binding and that binding of gentamicin to this site inhibits the chaperone activity of CRT.

Animals↗
PubMed2004

Structural basis of sugar-recognizing ubiquitin ligase.

SCF(Fbs1) is a ubiquitin ligase that functions in the endoplasmic reticulum (ER)-associated degradation pathway. Fbs1/Fbx2, a member of the F-box proteins, recognizes high-mannose oligosaccharides. Efficient binding to an N-glycan requires di-N-acetylchitobiose (chitobiose). Here we report the crystal structures of the sugar-binding domain (SBD) of Fbs1 alone and in complex with chitobiose. The SBD is composed of a ten-stranded antiparallel beta-sandwich. The structure of the SBD-chitobiose complex includes hydrogen bonds between Fbs1 and chitobiose and insertion of the methyl group of chitobiose into a small hydrophobic pocket of Fbs1. Moreover, NMR spectroscopy has demonstrated that the amino acid residues adjoining the chitobiose-binding site interact with the outer branches of the carbohydrate moiety. Considering that the innermost chitobiose moieties in N-glycans are usually involved in intramolecular interactions with the polypeptide moieties, we propose that Fbs1 interacts with the chitobiose in unfolded N-glycoprotein, pointing the protein moiety toward E2 for ubiquitination.

Amino Acid Sequence↗
PubMed2004

Temperature-dependent isologous Fab-Fab interaction that mediates cryocrystallization of a monoclonal immunoglobulin G.

Mechanisms of the cryoprecipitation of cryoglobulins have long been studied but not fully understood. In the present study, we characterize a monoclonal immunoglobulin G1 (IgG1) cryoglobulin that forms sharp needle crystals upon cooling and therefore might be an ideal example for the elucidation of a mechanism of cryoprecipitation of cryoglobulins. Limited proteolysis by papain of this cryoglobulin resulted in disappearance of cryocrystallization. Interactions of the proteolytic fragments were examined by surface plasmon resonance measurements. A temperature-dependent isologous Fab-Fab interaction was observed for this cryoglobulin. Glycosylation profiling by use of the HPLC mapping technique revealed that cryoglobulin expresses homogeneous N-glycans in its Fc portion. These results suggest that (1) the temperature-dependent crystallization of the cryoglobulin was ascribed to its specific Fab-Fab interaction and (2) the unusual homogeneity of the Fc glycosylation promote the crystallization of this cryoglobulin.

Cryoglobulins↗