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So Iwata

Publications and source records attributed to So Iwata.

14 recordsLinked to original sources
PubMed2003

Crystallization of the chaperonin GroEL-GroES complex from Thermus thermophilus HB8.

The chaperonin GroEL-GroES (GroEL/ES) complex from a thermophilic eubacteria, Thermus thermophilus HB8, has been purified and crystallized. The GroEL/ES complex is known to be composed of 14 identical GroEL subunits (58 kDa) and seven identical GroES subunits (11 kDa). The GroEL/ES complex crystals belong to the triclinic space group P1, with unit-cell parameters a = 140.4, b = 156.4, c = 273.1 A, alpha = 82.9, beta = 85.4, gamma = 68.5 degrees. The crystal asymmetric unit contains two molecules (MW = 885 kDa). One data set to 3.0 A resolution, with 383 652 independent observations (89.3% complete) and an R(merge) of 0.08, has been collected from a single crystal. A molecular-replacement solution was obtained using the structure of the GroEL/ES complex from Escherichia coli as a search model.

Chaperonin 10↗
PubMed2003

Structure and mechanism of the lactose permease of Escherichia coli.

Membrane transport proteins that transduce free energy stored in electrochemical ion gradients into a concentration gradient are a major class of membrane proteins. We report the crystal structure at 3.5 angstroms of the Escherichia coli lactose permease, an intensively studied member of the major facilitator superfamily of transporters. The molecule is composed of N- and C-terminal domains, each with six transmembrane helices, symmetrically positioned within the permease. A large internal hydrophilic cavity open to the cytoplasmic side represents the inward-facing conformation of the transporter. The structure with a bound lactose homolog, beta-D-galactopyranosyl-1-thio-beta-D-galactopyranoside, reveals the sugar-binding site in the cavity, and residues that play major roles in substrate recognition and proton translocation are identified. We propose a possible mechanism for lactose/proton symport (co-transport) consistent with both the structure and a large body of experimental data.

Amino Acid Substitution↗
PubMed2003

Protonmotive force generation by a redox loop mechanism.

Respiration involves the oxidation and reduction of substrate for the redox-linked formation of a protonmotive force (PMF) across the inner membrane of mitochondria or the plasma membrane of bacteria. A mechanism for PMF generation was first suggested by Mitchell in his chemiosmotic theory. In the original formulations of the theory, Mitchell envisaged that proton translocation was driven by a 'redox loop' between two catalytically distinct enzyme complexes. Experimental data have shown that this redox loop does not operate in mitochondria, but has been confirmed as an important mechanism in bacteria. The nitrate respiratory pathway in Escherichia coli is a paradigm for a protonmotive redox loop. The structure of one of the enzymes in this two-component system, formate dehydrogenase-N, has revealed the structural basis for the PMF generation by the redox loop mechanism and this forms the basis of this review.

Cell Respiration↗
PubMed2003

Variation in proton donor/acceptor pathways in succinate:quinone oxidoreductases.

The anaerobically expressed fumarate reductase and aerobically expressed succinate dehydrogenase from Escherichia coli comprise two different classes of succinate:quinone oxidoreductases (SQR), often termed respiratory complex II. The X-ray structures of both membrane-bound complexes have revealed that while the catalytic/soluble domains are structurally similar the quinone binding domains of the enzyme complexes are significantly different. These results suggest that the anaerobic and aerobic forms of complex II have evolved different mechanisms for electron and proton transfer in their respective membrane domains.

Benzoquinones↗
PubMed2003

Using rational screening and electron microscopy to optimize the crystallization of succinate:ubiquinone oxidoreductase from Escherichia coli.

The membrane-bound respiratory complex II, succinate:ubiquinone oxidoreductase (SQR) from Escherichia coli, has been anaerobically expressed, then purified and crystallized. The initial crystals obtained were small and diffracted poorly. In order to facilitate structure determination, rational screening and sample-quality analysis using electron microscopy was implemented. The crystals of SQR from E. coli belong to the trigonal space group R32, with unit-cell parameters a = b = 138.7, c = 521.9 A, and diffract to 2.6 A resolution. The optimization strategy used for obtaining well diffracting SQR crystals is applicable to a wide range of membrane proteins.

Anisotropy↗
PubMed2003

Architecture of succinate dehydrogenase and reactive oxygen species generation.

The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron acceptor, ubiquinone. It was found that the SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species (ROS) formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of ROS. Furthermore, symptoms of genetic disorders associated with mitochondrial SQR mutations may be a result of ROS formation resulting from impaired electron transport in the enzyme.

Aerobiosis↗
PubMed2003

Formate dehydrogenase--a versatile enzyme in changing environments.

Several structures belonging to the large bis-molybdopterin guanine dinucleotide enzyme family have been published during the past four years. These include the structures of three formate dehydrogenases containing intrinsic selenocysteine residues - two soluble enzymes and one integral membrane protein. Together these have given detailed structural and mechanistic information about this family of enzymes.

Amino Acid Sequence↗
PubMed2002

Golden mean to longevity: rareness of mitochondrial cytochrome b variants in centenarians but not in patients with Parkinson's disease.

To test the hypothesis that centenarians are free from deleterious mitochondrial variations, we analyzed amino acid variations in the cytochrome b molecule of 64 Japanese centenarians. Although the frequencies of some variations, such as N260D and G251S, differed significantly between centenarians and patients with Parkinson's disease, the most striking feature of centenarian cytochrome b was the rareness of amino acid variations in contrast to the variety of amino acid replacements in patients with Parkinson's disease. These results suggest that centenarians are genetically hitting the "golden mean" (less variation from the consensus cytochrome b sequence or less mismatch with other subunits). A multiplex detection system for various deleterious variations in combination with genetic tests for longevity-associated genotypes will be necessary to predict longevity or age-related diseases.

Adult↗
PubMed2002

The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides.

The structure of cytochrome c oxidase from Rhodobacter sphaeroides has been solved at 2.3/2.8A (anisotropic resolution). This high-resolution structure revealed atomic details of a bacterial terminal oxidase including water molecule positions and a potential oxygen pathway, which has not been reported in other oxidase structures. A comparative study of the wild-type and the EQ(I-286) mutant enzyme revealed structural rearrangements around E(I-286) that could be crucial for proton transfer in this enzyme. In the structure of the mutant enzyme, EQ(I-286), which cannot transfer protons during oxygen reduction, the side-chain of Q(I-286) does not have the hydrogen bond to the carbonyl oxygen of M(I-107) that is seen in the wild-type structure. Furthermore, the Q(I-286) mutant has a different arrangement of water molecules and residues in the vicinity of the Q side-chain. These differences between the structures could reflect conformational changes that take place upon deprotonation of E(I-286) during turnover of the wild-type enzyme, which could be part of the proton-pumping machinery of the enzyme.

Binding Sites↗
PubMed2002

Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.

The structure of the membrane protein formate dehydrogenase-N (Fdn-N), a major component of Escherichia coli nitrate respiration, has been determined at 1.6 angstroms. The structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 angstroms through the enzyme. The menaquinone reduction site associated with a possible proton pathway was also characterized. This structure provides critical insights into the proton motive force generation by redox loop, a common mechanism among a wide range of respiratory enzymes.

Binding Sites↗
PubMed2002

Purification, crystallisation and preliminary crystallographic studies of succinate:ubiquinone oxidoreductase from Escherichia coli.

A membrane protein complex, succinate dehydrogenase (SQR) from Escherichia coli has been purified and crystallised. This enzyme is composed of four subunits containing FAD, three iron-sulphur clusters and one haem b as prosthetic groups. The obtained crystals belong to the hexagonal space group P6(3) with the unit-cell dimensions of a=b=123.8 A and c=214.6 A. An asymmetric unit of the crystals contains one SQR monomer (M(r) 120 kDa). A data set is now available at 4.0 A resolution with 88.1% completeness and 0.106 R(merge). We have obtained a molecular replacement solution that shows sensible molecular packing, using the soluble domain of E. coli QFR (fumarate reductase) as a search model. The packing suggests that E. coli SQR is a crystallographic trimer rather than a dimer as observed for the E. coli QFR.

Crystallography↗
PubMed2002

Membrane protein complexes.

A wide range of membrane protein structures have been published during the past two years. These have included proteins from both eucaryotic and heterologously overexpressed sources. Whereas some of these proteins were crystallised using conventional techniques, others employed the new methods of lipidic cubic phase crystallisation and antibody fragment co-crystallisation. These and other new approaches to the expression and crystallisation of membrane proteins are accelerating structural studies of membrane protein complexes.

Bacterial Outer Membrane Proteins↗
PubMed2001

Purification and crystallization of the respiratory complex formate dehydrogenase-N from Escherichia coli.

A membrane-protein complex, formate dehydrogenase-N from Escherichia coli, has been purified and crystallized. This molybdenum-containing enzyme, composed of alpha, beta and gamma subunits, is the major electron donor to the nitrate respiratory chain of E. coli. The formate dehydrogenase-N crystals belong to the cubic space group P2(1)3, with unit-cell parameters a = b = c = 203 A. An asymmetric unit of the crystals is assumed to contain one formate dehydrogenase-N monomer (MW 170 kDa). One data set to 1.6 A resolution, with 342 711 independent observations (94.4% complete) and an R(merge) of 0.08, has been collected from a single crystal. This is the highest resolution data set reported for a membrane-protein complex to date.

Crystallization↗