The 1.3 A crystal structure of human mitochondrial Delta3-Delta2-enoyl-CoA isomerase shows a novel mode of binding for the fatty acyl group

The crystal structure of Delta3-Delta2-enoyl-CoA isomerase from human mitochondria (hmEci), complexed with the substrate analogue octanoyl-CoA, has been refined at 1.3 A resolution. This enzyme takes part in the beta-oxidation of unsaturated fatty acids by converting both cis-3 and trans-3-enoyl-CoA esters (with variable length of the acyl group) to trans-2-enoyl-CoA. hmEci belongs to the hydratase/isomerase (crotonase) superfamily. Most of the enzymes belonging to this superfamily are hexamers, but hmEci is shown to be a trimer. The mode of binding of the ligand, octanoyl-CoA, shows that the omega-end of the acyl group binds in a hydrophobic tunnel formed by residues of the loop preceding helix H4 as well as by side-chains of the kinked helix H9. From the structure of the complex it can be seen that Glu136 is the only catalytic residue. The importance of Glu136 for catalysis is confirmed by mutagenesis studies. A cavity analysis shows the presence of two large, adjacent empty hydrophobic cavities near the active site, which are shaped by side-chains of helices H1, H2, H3 and H4. The structure comparison of hmEci with structures of other superfamily members, in particular of rat mitochondrial hydratase (crotonase) and yeast peroxisomal enoyl-CoA isomerase, highlights the variable mode of binding of the fatty acid moiety in this superfamily.     

Structural transformation-mediated dimerization of caspase recruitment domain revealed by the crystal structure of CARD-only protein in frog virus 3

Caspase recruitment domain (CARD)-only proteins (COPs), regulate apoptosis, inflammation, and innate immunity. They inhibit the assembly of NOD-like receptor complexes such as the inflammasome and NODosome, which are molecular complexes critical for caspase-1 activation. COPs are known to interact with either caspase-1 CARD or RIP2 CARD via a CARD-CARD interaction, and inhibit caspase-1 activation or further downstream signaling. In addition to the human COPs, Pseudo-ICE, INCA, and ICEBERG, several viruses also contain viral COPs that help them escape the host immune system. To elucidate the molecular mechanism of host immunity inhibition by viral COPs, we solved the structure of a viral COP for the first time. Our structure showed that viral COP forms a structural transformation-mediated dimer, which is unique and has not been reported in any structural study of a CARD domain. Based on the current structure, and the previously solved structures of other death domain superfamily members, we propose that structural transformation-mediated dimerization might be a new strategy for dimer assembly in the death domain superfamily.     

The crystal structure of an EST2 mutant unveils structural insights on the H group of the carboxylesterase/lipase family

Esterase 2 (EST2) from the thermophilic eubacterium Alicyclobacillus acidocaldarius is a thermostable serine hydrolase belonging to the H group of the esterase/lipase family. This enzyme hydrolyzes monoacylesters of different acyl-chain length and various compounds with industrial interest. EST2 displays an optimal temperature at 70 degrees C and maximal activity with pNP-esters having acyl-chain bearing from six to eight carbon atoms. EST2 mutants with different substrate specificity were also designed, generated by site-directed mutagenesis, and biochemically characterized. To better define at structural level the enzyme reaction mechanism, a crystallographic analysis of one of these mutants, namely M211S/R215L, was undertaken. Here we report its three-dimensional structure at 2.10A resolution. Structural analysis of the enzyme revealed an unexpected dimer formation as a consequence of a domain-swapping event involving its N-terminal region. This phenomenon was absent in the case of the enzyme bound to an irreversible inhibitor having optimal substrate structural features. A detailed comparison of the enzyme structures before and following binding to this molecule showed a movement of the N-terminal helices resulting from a trans-cis isomerization of the F37-P38 peptide bond. These findings suggest that this carboxylesterase presents two distinct structural arrangements reminiscent of the open and closed forms already reported for lipases. Potential biological implications associated with the observed quaternary reorganization are here discussed in light of the biochemical properties of other lipolytic members of the H group.     

Crystal structure of the Ig1 domain of the neural cell adhesion molecule NCAM2 displays domain swapping

The crystal structure of the first immunoglobulin (Ig1) domain of neural cell adhesion molecule 2 (NCAM2/OCAM/RNCAM) is presented at a resolution of 2.7 Å. NCAM2 is a member of the immunoglobulin superfamily of cell adhesion molecules (IgCAMs). In the structure, two Ig domains interact by domain swapping, as the two N-terminal β-strands are interchanged. β-Strand swapping at the terminal domain is the accepted mechanism of homophilic interactions amongst the cadherins, another class of CAMs, but it has not been observed within the IgCAM superfamily. Gel-filtration chromatography demonstrated the ability of NCAM2 Ig1 to form dimers in solution. Taken together, these observations suggest that β-strand swapping could have a role in the molecular mechanism of homophilic binding for NCAM2.     

Delta 3,delta 2-enoyl-CoA isomerases. Characterization of the mitochondrial isoenzyme in the rat

Delta 3,delta 2-Enoyl-CoA isomerase (EC 5.3.3.8), an obligatory auxiliary enzyme for the metabolism of double bonds at odd-numbered positions of fatty acids during their beta-oxidation, was studied in hearts and livers of normal and clofibrate-treated rats. Hepatic peroxisomal and mitochondrial isoenzymes were separable by dye-ligand chromatography. The mitochondrial one was further purified to apparent homogeneity. An isomerase was also purified from heart muscle, a peroxisome-poor tissue. These enzymes were dimeric basic proteins (pI 9.5) with a subunit molecular weight of 30,000. Both cis- and trans-enoyl-CoA served as substrates for the hepatic enzyme studied. The velocity ratio for the C6-, C10-, and C12-trans-3-enoyl substrates was 9:2.5:1. By immunoelectron microscopy the enzyme protein selected for purification was found to be mitochondrial both in liver and heart. Chromatographic evidence, immunoelectron microscopy, and immunoblotting indicated that in the liver but not in the heart, the enzyme underwent an induction of 1 order of magnitude during clofibrate treatment. Antibodies towards the rat isomerases detected cross-reactive proteins in bovine and pig liver and heart and human placenta. The estimated subunit sizes varied from species to species, being 31,000 in bovine liver and heart, 29,000 in pig liver and heart, and 30,000 in human placenta. The data are in accord with the notion of a dual location of the delta 3,delta 2-enoyl-CoA isomerase. Mitochondrial origin of one of the isoenzymes and its tissue-specific induction by clofibrate were verified by immunochemistry and the identity of the peroxisomal one revealed by the chromatographic behavior of the proteins.     

Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism

The methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently, the genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes a conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). Herein, we report the crystal structures of B. subtilis M1Pi (Bs-M1Pi) in complex with its product MTRu-1-P, and a sulfate at 2.4 and 2.7 A resolution, respectively. The electron density clearly shows the presence of each compound in the active site. The structural comparison with other homologous proteins explains how the substrate uptake of Bs-M1Pi may be induced by an open/closed transition of the active site. The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi.     

Insights into sucrose isomerization from crystal structures of the Pseudomonas mesoacidophila MX-45 sucrose isomerase,MutB

Three-dimensional structures of a sucrose isomerase from Pseudomonas mesoacidophila MX-45, forming mainly trehalulose have been solved to resolutions in the range 1.8–2.2 Å. Native and mutant complexes give, for the first time, a thorough insight into substrate binding and recognition, and product specificities of these enzymes. This study has pinpointed essential residues for binding the substrate sucrose, and hereby given detailed information on the interactions between the enzyme active site and glucosyl- and fructosyl moieties. Moreover, the 3-D structures revealed an aromatic clamp formed by two phenylalanines, which plays an essential role in recognition of the substrate and in controlling the reaction specificity.     

Immunocytochemical localization of delta 3, delta 2-enoyl-CoA isomerase in rat liver. The effects of di-(2-ethylhexyl)phthalate, a peroxisome proliferator

Immunocytochemical localization of delta 3, delta 2-enoyl-CoA isomerase (isomerase) was investigated in rat liver. Livers of di-(2-ethylhexyl)phthalate (DEHP)-treated or untreated rats were perfusion-fixed and embedded in Epon or Lowicryl K4M. By light microscopy, reaction deposits for the enzyme were present in the cytoplasmic granules of hepatocytes and interlobular bile duct epithelium. Weak staining was noted in sinus-lining cells. After administration of DEHP, the granular staining of the hepatocytes was markedly enhanced, whereas the staining reaction of the sinus-lining cells decreased. The isomerase staining pattern was quite similar to that of long-chain acyl-CoA dehydrogenase (a mitochondrial marker), but different from that of catalase (a peroxisomal marker). Under electron microscopy, gold particles for isomerase were seen to be confined mainly to mitochondria of the hepatocytes, the bile duct epithelial cells and sinus-lining cells. Peroxisomes were weakly labeled. After DEHP administration, the peroxisomes were markedly induced, but the mitochondria were not. Quantitative analysis showed that the induction of the peroxisomal isomerase was only 2-fold whereas the mitochondrial isomerase was enhanced about 5-fold, 40 times as high as the peroxisomal enzyme. The results show that the mitochondria are the main intracellular site for isomerase and the peroxisomes a minor site. The mitochondrial isomerase of the rat liver is markedly induced by peroxisome proliferators, DEHP and clofibrate.     

A new crystal form of the NK1 splice variant of HGF/SF demonstrates extensive hinge movement and suggests that the NK1 dimer originates by domain swapping

NK1 is a splice variant of the polypeptide growth factor HGF/SF that consists of the N terminal (N) and first kringle (K) domains and retains receptor binding and signalling. While NK1 behaves as a monomer in solution, two independent crystallographic structures have previously shown an identical, tightly packed dimer. Here we report a novel orthorhombic crystal form of NK1 at 2.5 A resolution in which four NK1 protomers are packed in two distinct dimers in the asymmetric unit. Although the basic architecture of the new NK1 dimers is similar to the two described earlier, the new crystal form demonstrates extensive hinge movement between the N and K domain that leads to re-orientation of the receptor-binding sites. The hinge bending is evidence of the paucity of strong interactions between domains within the protomer, in contrast to the extensive interactions between protomers in the dimer. These observations are consistent with domain swapping in the dimer, such that the interdomain interactions of the monomer are replaced by equivalent interprotomer interactions in the dimer and offer a route for protein engineering of NK1 variants which may act as receptor antagonists.     

木糖异构酶序列结构特点、耐热机理及分子改造研究进展

近年来,随着发展低碳经济的迫切需要,可再生资源利用研究方兴未艾,其中,构建充分利用木质纤维素水解产物木糖生产乙醇的重组菌成为研究热点.木糖异构酶由于不需要辅酶,成为构建利用木糖重组酵母的首选途径.文中对近年来木糖异构酶的研究进展进行了综述.首先介绍了木糖异构酶的基本性质、序列、结构和功能特性,然后对其耐热机理进行了总结归纳;重点阐述了基于序列及结构进行的酶分子改造研究,包括底物特异性改造、热稳定性改造等;同时,结合作者的研究经历,对如何提高嗜热木糖异构酶在常温下的活性进行了探讨.最后,对木糖异构酶的研究进展进行了总结和展望,对基于结构改善木糖异构酶催化活性及构建新型高效利用木糖生产乙醇的重组菌具有重要的指导意义.     

Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine

Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. The native enzyme is a mixture of two dimeric forms with distinct structural features. The most abundant form is characterized by the swapping of N-terminal fragments. In this paper, the crystal structure of the complex between the swapping dimer and uridylyl(2',5')adenosine is reported at 2.06 A resolution. The refined model has a crystallographic R-factor of 0.184 and good stereochemistry. The quality of the electron density maps enables the structure of both the inhibitor and active site residues to be unambiguously determined. The overall architecture of the active site is similar to that of RNase A. The dinucleotide adopts an extended conformation with the pyrimidine and purine base interacting with Thr45 and Asn71, respectively. Several residues (Gln11, His12, Lys41, His119, and Phe120) bind the oxygens of the phosphate group. The structural similarity of the active sites of BS-RNase and RNase A includes some specific water molecules believed to be relevant to catalytic activity. Upon binding of the dinucleotide, small but significant modifications of the tertiary and quaternary structure of the protein are observed. The ensuing correlation of these modifications with the catalytic activity of the enzyme is discussed.     

The crystal structure of Arabidopsis thaliana RAC7/ROP9: the first RAS superfamily GTPase from the plant kingdom

Arabidopsis thaliana RAC/ROP GTPases constitute a plant specific Rho GTPase family in the RAS superfamily, which has been implicated in numerous pivotal signalling cascades in plants. Research has shown that plants in some cases have evolved different modes of regulating Rho GTPase activity as compared to the equivalent systems in animals and yeast. In order to gain structural insight into plant signaling at the molecular level, we have determined the first crystal structure of a RAC-like GTPase belonging to the RAS superfamily from the plant kingdom. The structure of AtRAC7/ROP9 bound to GDP was solved at a resolution of 1.78 A. We have found that the structure of plant Rho GTPases is based upon a conserved G-domain architecture, but structural differences were found concerning the insert region and switch II region of the protein.     

The crystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 1 represents a conformational intermediate in the reductive activation mechanism of the tetrameric enzyme

Toxoplasma gondii nucleoside triphosphate diphosphohydrolase (NTPDase) 1 was crystallized in an intermediate tetrameric conformation. The crystal structure is similar to that of T. gondii NTPDase3 and represents an inactive conformation as the activating disulfide bridge is not reduced and the active site cleft between the two domains of each monomer is open. However, the arrangement of the monomers within the tetramer differs from that of the inactive form of NTPDase3 and may represent an intermediate conformation on the path of the closure motion of the tetramer induced upon activation. Proteins 2013; 81:1271–1276. © 2013 Wiley Periodicals, Inc.     

Dynamical dimer structure and liquid structure of fatty acids in their binary liquid mixture: decanoic/octadecanoic acid and decanoic/dodecanoic acid systems

Dimer structure and liquid structure of fatty acids in their binary mixtures such as decanoic acid (DA)/octadecanoic acid (SA) and DA/dodecanoic acid (LA) were studied through the measurements of self-diffusion coefficient (D), differential scanning calorimetry (DSC), density and viscosity. The obtained phase diagrams showed that DA and SA form a eutectic in the solid state but partly a solid solution in the SA-rich region; DA and LA form an incongruent-melting compound which forms a eutectic with DA. In the liquid mixture of DA and SA, the D of DA is larger than that of SA over the entire range of compositions and tends to approach the D of SA with increasing SA-mole fraction; the D of DA in the DA/LA system is also larger than that of LA especially in the LA-poor region and steeply approaches that of LA with increasing LA-mole fraction. These D values and phase diagrams were compared with those for the binary mixtures of n-alkanes (C14/C20, C19/C20 and C20/C24); it is concluded that the two kinds of fatty acids always form their individual homodimers in their liquid mixtures regardless of their compositions and temperatures.     

Dynamical dimer structure and liquid structure of fatty acids in their binary liquid mixture: dodecanoic and 3-phenylpropionic acids system

Dimer structure and liquid structure of fatty acids in the binary liquid mixture of dodecanoic (LA) and 3-phenylpropionic acids (PPA) were studied through the measurements of DSC, self-diffusion coefficient (D), density, viscosity, 13C NMR spin-lattice relaxation time, small-angle X-ray scattering (SAXS), and small-angle neutron scattering (SANS). The phase diagram of LA/PPA mixture exhibited a typical eutectic pattern, which means that LA and PPA are completely immiscible in solid phase. In the liquid phase of the LA/PPA mixture, D of LA always differed from that of PPA irrespective of their compositions. This exhibited that, in the liquid phase of the binary mixture of fatty acids giving a complete eutectic in the solid phase, the fatty acid dimers are composed of the same fatty acid species irrespective of their compositions. The liquid structure of the LA/PPA mixture was clarified through the SAXS and also the SANS measurements.     

Partial purification and properties of a cis-3: trans-2-enal isomerase from cucumber fruit

An enzyme, which catalyses the isomerisation of cis-3-enals to trans-2-enals, has been partially purified from cucumber fruit. The isomerase activity has been resolved from significant contamination by the related activities, lipoxygenase and hydroperoxide cleavage enzymes. An examination of the substrate specificity of the isomerase enzyme showed it to be specific for the cis-3-enals. The most efficient isomerisation was achieved with cis-3-hexenal and cis-3-nonenal which are, physiologically, the two most significant substrates. The trans-3-enal and cis-3-enol were not suitable substrates for the enzyme.     

Competition between 24:5n-3 and ALA for Delta 6 desaturase may limit the accumulation of DHA in HepG2 cell membranes

The use of Delta 6 desaturase (D6D) twice in the conversion of alpha-linolenic acid (ALA; 18:3n-3) to docosahexaenoic acid (DHA; 22:6n-3) suggests that this enzyme may play a key regulatory role in the synthesis and accumulation of DHA from ALA. We examined this using an in vitro model of fatty acid metabolism to measure the accumulation of the long-chain metabolites of ALA in HepG2 cell phospholipids. The accumulation of ALA, eicosapentaenoic acid (20:5n-3), docosapentaenoic acid (22:5n-3), and 24:5n-3 in cell phospholipids was linearly related to the concentration of supplemented ALA over the range tested (1.8-72 microM). The accumulation of the post-D6D products of 22:5n-3, 24:6n-3 and DHA, in cell phospholipids was saturated at concentrations of >18 microM ALA. Supplementation of HepG2 cells with preformed DHA revealed that, although the accumulation of DHA in cell phospholipids approached saturation, the level of DHA in cell phospholipids was significantly greater compared with the accumulation of DHA from ALA, indicating that the accumulation of DHA from ALA was not limited by incorporation. The parallel pattern of accumulation of 24:6n-3 and DHA in response to increasing concentrations of ALA suggests that the competition between 24:5n-3 and ALA for D6D may contribute to the limited accumulation of DHA in cell membranes.     

Regular left-handed fragment of amylose: crystal and molecular structure of methyl-α-maltotrioside, 4H2O

The crystal structure of methyl-α-maltotrioside tetrahydrate C₁₆H₃₄O₁₆, 4H₂O), has been established by direct methods from 2269 independent reflections and refined to a final R value of 0.054. The crystal belongs to the orthorhombic system, space group P2₁2₁2₁ and has a unit cell of dimensions: a = 1.037 (1), b = 2.439 (1) and c = 1.065 (1) nm. The three glucose residues have the ⁴C₁ pyranose conformation and are α-(1–4)-linked. The conformation of the glycosidic linkage is characterized by torsion angles (φ, ψ) which take the values (82.2, −148.9) between the non-reducing and the middle residue and (82.8, −151.8) between the middle residue and the reducing one. The primary hydroxyl groups exist in a gauche-gauche conformation. This structure is also characterized by the lack of intramolecular hydrogen bonding between secondary hydroxyl groups belonging to contiguous residues. The molecules are held together by a complicated network of hydrogen bonds involving all the hydroxylic groups and the water molecules. the three dimensional arrangement corresponds to a regular alternation of antiparallel bilayers strongly linked by water molecules. A survey of the distribution of the glycosidic torsion angles in all known linear α-(1–4)-linked d-glucose residues, discloses the existence of three stable conformers. This crystal structure provides the first experimental evidence of a regular left-handed fragment of the amylosic chain in a highly hydrated neighbourhood. Furthermore, the helical conformation adopted by the trisaccharide gives rise to helical parameters which are close to those found experimentally for native A and B amyloses. The relevance of the present results to the rationalization of the polymorphic transformation of amylose, along with its crystallization habits is also discussed.