scholarly journals The Molecular Architecture of Galactose Mutarotase/UDP-Galactose 4-Epimerase from Saccharomyces cerevisiae

2005 ◽  
Vol 280 (23) ◽  
pp. 21900-21907 ◽  
Author(s):  
James B. Thoden ◽  
Hazel M. Holden
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Active Sites ◽  
Polypeptide Chain ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Dual Function ◽  
Molecular Architecture ◽  
Single Polypeptide Chain ◽  
Leloir Pathway ◽  
The Individual

The metabolic pathway by which β-d-galactose is converted to glucose 1-phosphate is known as the Leloir pathway and consists of four enzymes. In most organisms, these enzymes appear to exist as soluble entities in the cytoplasm. In yeast such as Saccharomyces cerevisiae, however, the first and last enzymes of the pathway, galactose mutarotase and UDP-galactose 4-epimerase, are contained within a single polypeptide chain referred to as Gal10p. Here we report the three-dimensional structure of Gal10p in complex with NAD+, UDP-glucose, and β-d-galactose determined to 1.85-Å resolution. The enzyme is dimeric with dimensions of ∼91 Å × 135 Å × 108 Å and assumes an almost V-shaped appearance. The overall architecture of the individual subunits can be described in terms of two separate N- and C-terminal domains connected by a Type II turn formed by Leu-357 to Val-360. The first 356 residues of Gal10p fold into the classical bilobal topology observed for all other UDP-galactose 4-epimerases studied thus far. This N-terminal domain contains the binding sites for NAD+ and UDP-glucose. The polypeptide chain extending from Glu-361 to Ser-699 adopts a β-sandwich motif and harbors the binding site for β-d-galactose. The two active sites of Gal10p are separated by over 50 Å. This investigation represents the first structural analysis of a dual function enzyme in the Leloir pathway.

The three-dimensional structure of crystalline porcine pancreatic elastase

1970 ◽  
Vol 257 (813) ◽  
pp. 111-118 ◽  
Keyword(s):  
Amino Acid ◽  
Catalytic Mechanism ◽  
Polypeptide Chain ◽  
Molecular Model ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Side Chains ◽  
Peptide Bonds ◽  
Single Polypeptide Chain ◽  
Single Polypeptide

Elastase is a proteolytic enzyme obtained from pig pancreas, which shows a high degree of amino acid sequence homology with other serine proteinases, including bovine trypsin and chymotrypsin (Hartley, this volume, p. 77). It consists of a single polypeptide chain of 240 residues, which corresponds to the single polypeptide chain of trypsin, and the B and C chains of chymotrypsin. Elastase possesses a common catalytic mechanism with these enzymes but differs from them in its substrate specificity, cleaving peptide bonds on the carboxyl terminal side of amino acid residues lacking charged or aromatic side chains (Naughton & Sanger 1961). Several workers have suggested that homologous enzymes with common catalytic mechanisms have very similar tertiary structures. This prediction was supported by Blow and his co-workers, who found that the two disulphide bridges present in trypsin, but absent in chymotrypsin, could be built into the molecular model of a-chymotrypsin with little or no distortion of the polypeptide chain (Sigler, Blow, Matthews & Henderson 1968), and by Hartley (this volume, p. 77) who has shown that the trypsin and elastase side chains can be substituted for those present in a skeletal molecular model of a-chymotrypsin with no gross distortions of the polypeptide chain.

The three-dimensional structure of interleukin-1β

1988 ◽  
Vol 16 (6) ◽  
pp. 949-953 ◽  
Author(s):  
JOHN P. PRIESTLE ◽  
HANS-PETER SCHÄR ◽  
MARKUS G. GRÜTTER
Keyword(s):  
Polypeptide Chain ◽  
Three Dimensional ◽  
Interleukin 1Β ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
R Factor ◽  
The Core ◽  
Internal Sequence ◽  
Network Of Hydrogen Bonds

Summary The three-dimensional structure of human recombinant interleukin-1β has been determined at 0.24 nm resolution by X-ray crystallographic techniques. The partially refined model has a crystallographic R-factor of just under 19%. The structure is composed of 12 β-strands forming a complex network of hydrogen bonds. The core of the structure can best be described as a tetrahedron whose edges are each formed by two antiparallel β-strands. The interior of this structure is filled with hydrophobic side-chains. There is a 3-fold repeat in the folding of the polypeptide chain. Although this folding pattern suggests gene triplication, no significant internal sequence homology between topologically corresponding residues exists. The folding topology of interleukin-1β is very similar to that described by A. D. McLachlan [(1979) J. Mol. Biol. 133, 557–563] for soybean trypsin inhibitor.

On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase

1981 ◽  
Vol 293 (1063) ◽  
pp. 159-171 ◽  
Keyword(s):  
Catalytic Mechanism ◽  
Polypeptide Chain ◽  
Three Dimensional ◽  
Triose Phosphate Isomerase ◽  
Dimensional Structure ◽  
Dihydroxyacetone Phosphate ◽  
Triose Phosphate ◽  
Independent Determination ◽  
Chicken Muscle

Triose phosphate isomerase is a dimeric enzyme of molecular mass 56000 which catalyses the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde-3-phosphate. The crystal structure of the enzyme from chicken muscle has been determined at a resolution of 2.5 A, and an independent determination of the structure of the yeast enzyme has just been completed at 3 A resolution. The conformation of the polypeptide chain is essentially identical in the two structures, and consists of an inner cylinder of eight strands of parallel |3-pleated sheet, with mostly helical segments connecting each strand. The active site is a pocket containing glutamic acid 165, which is believed to act as a base in the reaction. Crystallographic studies of the binding of DHAP to both the chicken and the yeast enzymes reveal a common mode of binding and suggest a mechanism for catalysis involving polarization of the substrate carbonyl group.

scholarly journals Three-Dimensional Structure of PANI/CdS NRs-SiO2 Hydrogel for Photocatalytic Hydrogen Evolution with High Activity and Stability

Nanomaterials ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 427 ◽  
Author(s):  
Jinrong Lu ◽  
Xin Zhang ◽  
Huiyuan Gao ◽  
Wenquan Cui
Keyword(s):  
Hydrogen Production ◽  
Active Sites ◽  
Production Efficiency ◽  
Conductive Polymer ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Composite Catalyst ◽  
Binary Complex ◽  
Three Dimensional Structure ◽  
Cds Nanorods

Three-dimensional PANI/CdSNRs-SiO2 hydrogel (CdS NRs-PANI-SiO2) was synthesized by loading polyaniline (PANI) onto the semiconductor CdS nanorods (NRs) surface and loading the binary complex on SiO2 gel. The structure, optical properties, and electrochemical properties of the composite were studied in detail. The hydrogen production amount of CdS NRs-PANI (3%)-SiO2 (20%) increased in comparison with CdS NRs and reached 43.25 mmol/g in 3 h under visible light. The three-dimensional structure of SiO2 hydrogel increased the specific surface area of the catalyst, which was conducive to exposing more active sites of the catalyst. In addition, the conductive polymer PANI coated on CdS NRs played the role of conductive charge and effectively inhibited the photo-corrosion of CdS NRs. In addition, the recovery experiment showed that the recovery rate of the composite catalyst reached 90% and hydrogen production efficiency remained unchanged after five cycles, indicating that the composite catalyst had excellent stability.

scholarly journals RNA minihelices as model substrates for ATP/CTP:tRNA nucleotidyltransferase

1997 ◽  
Vol 327 (3) ◽  
pp. 847-851 ◽  
Author(s):  
Zengji LI ◽  
Yue SUN ◽  
L. David THURLOW
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Single Base ◽  
Three Dimensional Structure ◽  
E Coli ◽  
Base Identity

Twenty-one RNA minihelices, resembling the coaxially stacked acceptor- /T-stems and T-loop found along the top of a tRNA's three-dimensional structure, were synthesized and used as substrates for ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and Saccharomyces cerevisiae. The sequence of nucleotides in the loop varied at positions corresponding to residues 56, 57 and 58 in the T-loop of a tRNA. All minihelices were substrates for both enzymes, and the identity of bases in the loop affected the interaction. In general, RNAs with purines in the loop were better substrates than those with pyrimidines, although no single base identity absolutely determined the effectiveness of the RNA as substrate. RNAs lacking bases near the 5ʹ-end were good substrates for the E. coli enzyme, but were poor substrates for that from yeast. The apparent Km values for selected minihelices were 2-3 times that for natural tRNA, and values for apparent Vmax were lowered 5-10-fold.

scholarly journals Molecular architecture of inner dynein arms in situ in Chlamydomonas reinhardtii flagella

2008 ◽  
Vol 183 (5) ◽  
pp. 923-932 ◽  
Author(s):  
Khanh Huy Bui ◽  
Hitoshi Sakakibara ◽  
Tandis Movassagh ◽  
Kazuhiro Oiwa ◽  
Takashi Ishikawa
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Molecular Architecture ◽  
Heavy Chains ◽  
Distal Side ◽  
Cryo Electron Tomography ◽  
Dynein Arms

The inner dynein arm regulates axonemal bending motion in eukaryotes. We used cryo-electron tomography to reconstruct the three-dimensional structure of inner dynein arms from Chlamydomonas reinhardtii. All the eight different heavy chains were identified in one 96-nm periodic repeat, as expected from previous biochemical studies. Based on mutants, we identified the positions of the AAA rings and the N-terminal tails of all the eight heavy chains. The dynein f dimer is located close to the surface of the A-microtubule, whereas the other six heavy chain rings are roughly colinear at a larger distance to form three dyads. Each dyad consists of two heavy chains and has a corresponding radial spoke or a similar feature. In each of the six heavy chains (dynein a, b, c, d, e, and g), the N-terminal tail extends from the distal side of the ring. To interact with the B-microtubule through stalks, the inner-arm dyneins must have either different handedness or, more probably, the opposite orientation of the AAA rings compared with the outer-arm dyneins.

scholarly journals Phenylalanine ammonia-lyase (PAL) from tobacco (Nicotiana tabacum): characterization of the four tobacco PAL genes and active heterotetrameric enzymes1

2009 ◽  
Vol 424 (2) ◽  
pp. 233-242 ◽  
Author(s):  
Angelika I. Reichert ◽  
Xian-Zhi He ◽  
Richard A. Dixon
Keyword(s):  
Nicotiana Tabacum ◽  
Phenylalanine Ammonia Lyase ◽  
Consensus Sequence ◽  
Three Dimensional ◽  
Pcr Amplification ◽  
Dimensional Structure ◽  
Kinetic Properties ◽  
Cdna Clones ◽  
Phenylpropanoid Biosynthesis ◽  
The Individual

PAL (L-phenylalanine ammonia-lyase), the first enzyme of phenylpropanoid biosynthesis, is often encoded by multigene families in plants. A PCR-based approach was used to isolate cDNA clones corresponding to the four PAL genes of tobacco (Nicotiana tabacum). By careful comparison of cDNA and genomic clones, a new PAL gene (PAL4) was defined. PCR amplification of PAL sequences from cDNA led to the generation of chimaeric clones between PAL1 and PAL4, and incorrect annotation of PAL4 ESTs (expressed sequence tags) as PAL1 in the EST database has given rise to a randomly shuffled tentative consensus sequence. The PAL2 previously described in the literature was shown, by domain swapping experiments with PAL1, to possess a single nucleotide substitution leading to an inactive enzyme. The altered amino acid resulting from this substitution maps to the base of the active site pocket in the three-dimensional structure of PAL. The inactive PAL2 allele could not be recovered from 13 different tobacco cultivars examined. PALs 1–4 were co-expressed in multiple plant organs, and were also co-induced following exposure of cell cultures to yeast elicitor or methyl jasmonate. All four tobacco PAL proteins expressed in Escherichia coli displayed normal Michaelis–Menten kinetics, with Km values between 36 and 60 μM. Co-expression of different PAL proteins in E. coli resulted in formation of heterotetramers, which possessed kinetic properties within the same range as those of the individual homotetramers. The potential physiological function of heterotetrameric PAL forms is discussed.

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