Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution

The molecular structure of cytoplasmic malate dehydrogenase from pig heart has been refined by alternating rounds of restrained least-squares methods and model readjustment on an interactive graphics system. The resulting structure contains 333 amino acids in each of the two subunits, 2 NAD molecules, 471 solvent molecules, and 2 large noncovalently bound molecules that are assumed to be sulfate ions. The crystallographic study was done on one entire dimer without symmetry restraints. Analysis of the relative position of the two subunits shows that the dimer does not obey exact 2-fold rotational symmetry; instead, the subunits are related by a 173 degrees rotation. The structure results in a R factor of 16.7% for diffraction data between 6.0 and 2.5 A, and the rms deviations from ideal bond lengths and angles are 0.017 A and 2.57 degrees, respectively. The bound coenzyme in addition to hydrophobic interactions makes numerous hydrogen bonds that either are directly between NAD and the enzyme or are with solvent molecules, some of which in turn are hydrogen bonded to the enzyme. The carboxamide group of NAD is hydrogen bonded to the side chain of Asn-130 and via a water molecule to the backbone nitrogens of Leu-157 and Asp-158 and to the carbonyl oxygen of Leu-154. Asn-130 is one of the corner residues in a beta-turn that contains the lone cis peptide bond in cytoplasmic malate dehydrogenase, situated between Asn-130 and Pro-131. The active site histidine, His-186, is hydrogen bonded from nitrogen ND1 to the carboxylate of Asp-158 and from its nitrogen NE2 to the sulfate ion bound in the putative substrate binding site. In addition to interacting with the active site histidine, this sulfate ion is also hydrogen bonded to the guanidinium group of Arg-161, to the carboxamide group of Asn-140, and to the hydroxyl group of Ser-241. It is speculated that the substrate, malate or oxaloacetate, is bound in the sulfate binding site with the substrate 1-carboxyl hydrogen bonded to the guanidinium group of Arg-161.     

The three-dimensional structure of porcine heart mitochondrial malate dehydrogenase at 3.0-A resolution

In a previous study, we reported the apparent similarity between a low resolution electron density map of mitochondrial malate dehydrogenase and a model of cytoplasmic malate dehydrogenase (Roderick, S. L., and Banaszak, L. J. (1983) J. Biol. Chem. 258, 11636-11642). We have since determined the polypeptide chain conformation and coenzyme binding site of crystalline porcine heart mitochondrial malate dehydrogenase by x-ray diffraction methods. The crystals from which the diffraction data was obtained contain four subunits of the enzyme arranged as a "dimer of dimers," resulting in a crystalline tetramer which possesses 222 molecular symmetry. The overall polypeptide chain conformation of the enzyme, the location of the coenzyme binding site, and the preliminary location of several catalytically important residues have confirmed the structural similarity of mitochondrial malate dehydrogenase to cytoplasmic malate dehydrogenase and lactate dehydrogenase.     

Structure of actinidin: details of the polypeptide chain conformation and active site from an electron density map at 2-8 A resolution

A 2·8 Å resolution electron density map of the sulphydryl protease, actinidin, has been calculated. Two isomorphous heavy-atom derivatives, prepared with uranyl acetate and dichloroethylenediamineplatinum(II), were used to calculate phases by the method of isomorphous replacement, giving an overall figure of merit of 0·81. The polypeptide chain is well-defined in the present map and many side-chains can be identified from their appearance. The molecule consists of a single chain of 220 residues, the last two of which appear disordered in the map and contains at least two, and probably three, disulphide bridges. The conformation of the polypeptide chain is remarkably similar to that of papain. It is folded into two domains, domain I consisting of residues 19–115 and 214–218, and domain II residues 1–18 and 116–213. There are three significant stretches of α-helix, involving residues 25–42, 69–81 and 120–129, together with several shorter pieces, while much of domain II consists of a twisted β-sheet structure. When compared with papain, actinidin has two additional residues inserted between 59 and 60, one inserted between 78 and 79, and four between 168 and 169 (papain numbering) while one residue (194) has been deleted from the papain structure. All these changes are in external parts of the molecule and have little effect on the conformation. The positions and orientations of the catalytically-important side-chains in the active site are virtually identical with those in papain, but some of the side-chains lining the non-polar binding pocket are clearly different.     

Structure of yeast hexokinase. II. A 6 angstrom resolution electron density map showing molecular shape and heterologous interaction of subunits

An electron density map of yeast hexokinase has been calculated at 6 Å resolution using six heavy atom derivatives. The map shows each of the enzyme's two 51,000 molecular weight subunits to consist of two separate lobes connected by a narrow bridge of density. Furthermore, these two subunits are related to each other in the asymmetric unit of the crystal by a quasi-2-fold rather than a true 2-fold axis. That is, they are related by a rotation of 180 ° plus a relative translation of 3.6 Å along the symmetry axis. This gives rise to a heterologous subunit interaction and a possibility of non-identical structure and function for these chemically identical subunits. The molecule is quite asymmetric, having dimensions of 150 Å × 45 Å × 55 Å. Each subunit is about 80 Å × 40 Å × 50 Å.A portion of an electron density map at 3 Å resolution has been also calculated, based on phases from two heavy atom derivatives. Polypeptide backbone and side chains are visible in this map.     

NAD-dependent formate dehydrogenase of methylotrophic bacteria Pseudomonas sp. 101. II. Enzyme conformation at 3.0 A resolution

Three heavy atom isomorphous derivatives were used for the X-ray analysis of the holo form of NAD-dependent bacterial formate dehydrogenase (ternary complex enzyme-NAD-azide) at 3.0 A resolution. The enzyme subunit contains a catalytic and a coenzyme binding domain, with the active centre and the coenzyme binding site in the cleft between the domains. The polypeptide chain's fold and the position of 393 C alpha-atoms were determined. The secondary structure of the formate dehydrogenase was resolved. The structure of the NAD-binding domain is shown to be similar to that of other NAD-dependent enzymes.     

Structure of lobster apo-d-glyceraldehyde-3-phosphate dehydrogenase at 3.0 Å resolution

Lobster apo-glyceraldehyde-3-phosphate dehydrogenase was prepared by first lowering the pH to 4.8, thus reducing the NAD binding energy, and then separating the enzyme and coenzyme on a Sephadex column. Triclinic crystals were grown from an ammonium sulfate solution at pH 6.2. The apo-structure was initially determined approximately by comparison with the known hologlyceraldehyde-3-phosphate dehydrogenase molecule. The former was then refined using the 222 molecular symmetry with the molecular replacement technique. Only minor conformational differences were observed between apo and holo-glyceraldehyde-3-phosphate dehydrogenase. Trp193 in the “S loop” and the adenine-binding pocket showed the most significant changes.     

The nature of the substrate inhibition of cytoplasmic malate dehydrogenase from Phycomyces blakesleeanus

The mechanism that leads to substrate inhibition of cytoplasmic malate dehydrogenase (l-malate:NAD oxidoreductase, EC 1.1.1.37) from mycelium of Phycomyces blakesleeanus was investigated. A dead-end complex between enzyme and the enol-oxalacetate form appears to be responsible for this inhibition. The formation of the complex occurs more readily at acidic pH values. Results of this study suggest that the binding of oxalacetate as inhibitor prevent the NADH binding, with an estimated K_i for oxalacetate of 1.8 ± 0.1 mM. Such a competitive inhibition implies that the binding site for oxalacetate is the same both as inhibitor as well as substrate.     

Structure of an insect virus at 3.0 A resolution

We report the first atomic resolution structure of an insect virus determined by single crystal X-ray diffraction. Black beetle virus has a bipartite RNA genome encapsulated in a single particle. The capsid contains 180 protomers arranged on a T = 3 surface lattice. The quaternary organization of the protomers is similar to that observed in the T = 3 plant virus structures. The protomers consist of a basic, crystallographically disordered amino terminus (64 residues), a beta-barrel as seen in other animal and plant virus subunits, an outer protrusion composed predominantly of beta-sheet and formed by three large insertions between strands of the barrel, and a carboxy terminal domain composed of two distorted helices lying inside the shell. The outer surfaces of quasi-threefold related protomers form trigonal pyramidyl protrusions. A cleavage site, located 44 residues from the carboxy terminus, lies within the central cavity of the protein shell. The structural motif observed in BBV (a shell composed of 180 eight-stranded antiparallel beta-barrels) is common to all nonsatellite spherical viruses whose structures have so far been solved. This highly conserved shell architecture suggests a common origin for the coat protein of spherical viruses, while the primitive genome structure of BBV suggests that this insect virus represents an early stage in the evolution of spherical viruses from cellular genes.     

The reduction of aromatic alpha-keto acids by cytoplasmic malate dehydrogenase and lactate dehydrogenase

This study demonstrates that cytoplasmic malate dehydrogenase (MDH-s) catalyzes the reduction of aromatic alpha-keto acids in the presence of NADH, that the enzyme which has been described in the literature as aromatic alpha-keto acid reductase (KAR; EC 1.1.1.96) is identical to MDH-s, and that the reduction of aromatic alpha-keto acids is due predominantly to a previously unrecognized secondary activity of MDH-s and the remainder is due to the previously recognized activity of lactate dehydrogenase (LDH) toward aromatic keto-acids. MDH-s and KAR have the same molecular weight, subunit structure, and tissue distribution. Starch gel electrophoresis followed by histochemical staining using either p-hydroxy-phenylpyruvic acid (HPPA) or malate as the substrate shows that KAR activity comigrates with MDH-s in all species studied except some marine species. Inhibition with malate, the end product of the MDH reaction, substantially reduces or totally eliminates KAR activity. Genetically determined electrophoretic variants of MDH-s seen in the fresh water bony fish of the genus Xiphophorus and the amphibian Rana pipiens exhibited identical variation for KAR, and the two traits cosegregated in the offspring from one R. pipiens heterozygote studied. Both enzymes comigrate with no electrophoretic variation among several inbred strains of mice. Antisera raised against purified chicken MDH-s totally inhibited both MDH-s and KAR activity in chicken liver homogenates. There is no evidence to suggest that any protein besides MDH-s and LDH catalyzes this reaction with the possible exception of the situation in Xiphophorus, in which a third independent zone of HPPA reduction is observed. In most species the activity formerly described as KAR appears to be due to a previously unsuspected activity of MDH-s toward aromatic monocarboxylic alpha-keto acids. In all species examined the KAR activity is associated only with MDH-s; in tissue homogenates the mitochondrial form of MDH (MDH-m) is not detected after electrophoresis using HPPA as a substrate.     

Biochemical differences between cytoplasmic malate dehydrogenase allozymes of Drosophila virilis

Two allozymes (MDH^f and MDH^s) of cytoplasmic malate dehydrogenase of Drosophila virilis were partially purified and their biochemical properties were compared. MDH^f has a pH optimum of 9.75 and MDH^s one of 9.25 for malate oxidation. Optimal pH for oxaloacetate reduction is 6.75 and 8.0 for MDH^f and MDH^s, respectively. The K_m value for oxaloacetate of MDH^s is approximately twice as that of MDH^f. No differences were found with respect to thermostability and K_m's for malate, NAD⁺, or NADH. These results are discussed in terms of the physiological role of cytoplasmic malate dehydrogenase of D. virilis.This work was supported in part by grants from the Ministry of Education, Japan, Nos. 134050 and 154205.     

Localization of two phylloquinones, QK and QK', in an improved electron density map of photosystem I at 4-A resolution

An improved electron density map of photosystem I from Synechococcus elongatus calculated at 4-A resolution for the first time reveals a second phylloquinone molecule and thereby completes the set of cofactors constituting the electron transfer system of this iron-sulfur type photosynthetic reaction center: six chlorophyll a, two phylloquinones, and three Fe4S4 clusters. The location of the newly identified phylloquinone pair, the individual plane orientations of these molecules, and the resulting distances to other cofactors of the electron transfer system are discussed and compared with those determined by magnetic resonance techniques.     

23S rRNA assisted folding of cytoplasmic malate dehydrogenase is distinctly different from its self-folding

The role of the 50S particle of Escherichia coli ribosome and its 23S rRNA in the refolding and subunit association of dimeric porcine heart cytoplasmic malate dehydrogenase (s-MDH) has been investigated. The self-reconstitution of s-MDH is governed by two parallel pathways representing the folding of the inactive monomeric and the dimeric intermediates. However, in the presence of these folding modulators, only one first order kinetics was observed. To understand whether this involved the folding of the monomers or the dimers, subunit association of s-MDH was studied using fluorescein-5-isothiocyanate–rhodamine-isothiocyanate (FITC–RITC) fluorescence energy transfer and chemical cross-linking with gluteraldehyde. The observation suggests that during refolding the interaction of the unstructured monomers of s-MDH with these ribosomal folding modulators leads to very fast formation of structured monomers that immediately dimerise. These inactive dimers then fold to the native ones, which is the rate limiting step in 23S or 50S assisted refolding of s-MDH. Furthermore, the sequential action of the two fragments of domain V of 23S rRNA has been investigated in order to elucidate the mechanism. The central loop of domain V of 23S rRNA (RNA1) traps the monomeric intermediates, and when they are released by the upper stem–loop region of the domain V of 23S rRNA (RNA2) they are already structured enough to form dimeric intermediates which are directed towards the proper folding pathway.