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Pyridoxal-5'-phosphate (vitamin B 6 ) binding enzymes form a large superfamily that contains at least five different folds. The availability of an increasing number of known three-dimensional structures for members of this superfamily has allowed a detailed structural classification. Most progress has been made with the fold type I or aspartate aminotransferase family.
Background: E colicin proteins have three functional domains, each of which is implicated in one of the stages of killing Escherichia coli cells: receptor binding, translocation and cytotoxicity. The central (R) domain is responsible for receptor-binding activity whereas the N-terminal (T) domain mediates translocation, the process by which the C-terminal cytotoxic domain is transported from the receptor...
Background: RNA cyclases are a family of RNA-modifying enzymes that are conserved in eucarya, bacteria and archaea. They catalyze the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate. These enzymes might be responsible for production of the cyclic phosphate RNA ends that are...
Background: The fungal oxidoreductase cellobiose dehydrogenase (CDH) degrades both lignin and cellulose, and is the only known extracellular flavocytochrome. This haemoflavoenzyme has a multidomain organisation with a b-type cytochrome domain linked to a large flavodehydrogenase domain. The two domains can be separated proteolytically to yield a functional cytochrome and a flavodehydrogenase. Here,...
A selection of interesting papers that were published in the month before our press date in major journals most likely to report significant results in structural biology, protein and RNA folding.
Background: Members of the Rho family of small GTP-binding proteins, such as Rho, Rac and Cdc42, have a role in a wide range of cell responses. These proteins function as molecular switches by virtue of a conformational change between the GTP-bound (active) and GDP-bound (inactive) forms. In addition, most members of the Rho and Rac subfamilies cycle between the cytosol and membrane. The cytosolic...
Background: Transhydrogenase, located in the inner membranes of animal mitochondria and the cytoplasmic membranes of bacteria, couples the transfer of reducing equivalents between NAD(H) and NADP(H) to proton pumping. The protein comprises three subunits termed dI, dII and dIII. The dII component spans the membrane. The dI component, which contains the binding site for NAD + /NADH, and the...
Background: The 113-residue α+β protein suc1 is a member of the cyclin-dependent kinase subunit (cks) family of proteins that are involved in regulation of the eukaryotic cell cycle. In vitro, suc1 undergoes domain swapping to form a dimer by the exchange of a C-terminal β strand. We have analysed the folding pathway of suc1 in order to determine the atomic details of how strand-exchange occurs in...
Background: The p13suc1 gene product is a member of the cks (cyclin-dependent protein kinase subunit) protein family and has been implicated in regulation of the cell cycle. Various crystal structures of suc1 are available, including a globular, monomeric form and a β-strand exchanged dimer. It has been suggested that conversions between these forms, and perhaps others, may be important in the regulation...
Background: The Staphylococcus aureus collagen-binding protein Cna mediates bacterial adherence to collagen. The primary sequence of Cna has a non-repetitive collagen-binding A region, followed by the repetitive B region. The B region has one to four 23 kDa repeat units (B 1 -B 4 ), depending on the strain of origin. The affinity of the A region for collagen is independent of the B...
Background: Dihydroorotate dehydrogenase (DHODH) catalyzes the fourth committed step in the de novo biosynthesis of pyrimidines. As rapidly proliferating human T cells have an exceptional requirement for de novo pyrimidine biosynthesis, small molecule DHODH inhibitors constitute an attractive therapeutic approach to autoimmune diseases, immunosuppression, and cancer. Neither the structure of human...
Background: The bifunctional enzyme formiminotransferase-cyclodeaminase (FTCD) contains two active sites at different positions on the protein structure. The enzyme binds a γ-linked polyglutamylated form of the tetrahydrofolate substrate and channels the product of the transferase reaction from the transferase active site to the cyclodeaminase active site. Structural studies of this bifunctional enzyme...
Background: GDP-mannose 4,6 dehydratase (GMD) catalyzes the conversion of GDP-(d)-mannose to GDP-4-keto, 6-deoxy-(d)-mannose. This is the first and regulatory step in the de novo biosynthesis of GDP-(l)-fucose. Fucose forms part of a number of glycoconjugates, including the ABO blood groups and the selectin ligand sialyl Lewis X. Defects in GDP-fucose metabolism have been linked to leukocyte adhesion...
A selection of interesting papers that were published in the month before our press date in major journals most likely to report significant results in structural biology, protein and RNA folding.
Background: The l-aminopeptidase d-Ala-esterase/amidase from Ochrobactrum anthropi (DmpA) releases the N-terminal l and/or d-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both d and l stereospecificity. The DmpA active form is an αβ heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide.Results:...
Background: β-Ketoacyl-acyl carrier protein synthase III (FabH) initiates elongation in type II fatty acid synthase systems found in bacteria and plants. FabH is a ubiquitous component of the type II system and is positioned ideally in the pathway to control the production of fatty acids. The elucidation of the structure of FabH is important for the understanding of its regulation by feedback inhibition...
The phospholipases A 2 (PLA 2 s) are a large family of enzymes with varied lipidic products which are involved in numerous signal transduction pathways. The structural and functional characterization of several PLA 2 s have revealed the various mechanisms used by these enzymes to ingeniously manipulate the phospholipidic metabolic machinery.
Background: A novel bacterial esterase that cleaves esters on halogenated cyclic compounds has been isolated from an Alcaligenes species. This esterase 713 is encoded by a 1062 base pair gene. The presence of a leader sequence of 27 amino acids suggests that this enzyme is exported from the cytosol. Esterase 713 has been over-expressed in Agrobacterium without this leader sequence. Its amino acid...
Background: The protein farnesyltransferase (FTase) catalyzes addition of the hydrophobic farnesyl isoprenoid to a cysteine residue fourth from the C terminus of several protein acceptors that are essential for cellular signal transduction such as Ras and Rho. This addition is necessary for the biological function of the modified proteins. The majority of Ras-related human cancers are associated with...
Background: S100C (S100A11) is a member of the S100 calcium-binding protein family, the function of which is not yet entirely clear, but may include cytoskeleton assembly and dynamics. S100 proteins consist of two EF-hand calcium-binding motifs, connected by a flexible loop. Like several other members of the family, S100C forms a homodimer. A number of S100 proteins form complexes with annexins, another...
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