The reactions of pyridoxal 5′-phosphate with the M4 and H4 isoenzymes of pig lactate dehydrogenase

The H₄ and M₄ isoenzymes of pig lactate dehydrogenase are both inactivated by reaction with pyridoxal 5′-phosphate. In the early stages, inactivation is largely reversible by the addition of lysine in excess, but may be made irreversible by reduction with borohydride. This indicates that modification of lysine residues probably causes the initial inactivation. Both isoenzymes also undergo a slower process of irreversible inactivation which becomes more evident with increasing concentrations of pyridoxal 5′-phosphate and higher temperature. Although coenzymes give only partial protection of enzyme activity, they nevertheless completely prevent irreversible inactivation. Neither pyruvate nor lactate alone gives any protection. With the M₄ isoenzyme, complete protection against inactivation by pyridoxal 5′-phosphate may be achieved in ternary complexes, but no conditions have been found for complete protection of the H₄ isoenzyme. In the course of irreversible inactivation of H₄ lactate dehydrogenase, complete loss of activity can be correlated with the loss of approximately two free thiol groups per subunit. Present findings with regard to the importance of temperature and reagent concentration in determining the outcome of the chemical modification appear to resolve earlier controversy.     

Crystallization and preliminary crystallographic analysis at low resolution of the allosteric l-lactate dehydrogenase from Lactobacillus casei

The allosteric l-lactate dehydrogenase from Lactobacillus casei has been crystallized in its complex with the activators fructose-1,6-diphosphate and Co²⁺. The enzyme crystallizes in space group C2 with six tetramers in the unit cell. At very low resolution, 00l reflexions are absent for l ≠ 3n. The orientation of the molecular axes has been determined using the rotation function. All tetramers in the unit cell exhibit excellent 222 symmetry, and the overall arrangement resembles the packing that would be expected in the higher symmetry space group P3₁21. Comparison with the apo-enzyme structure of M4-lactate dehydrogenase from dogfish indicates high structural similarity between these enzymes and allowed us to identify the molecular axes of L. caseil-lactate dehydrogenase in terms of the “standard” molecular co-ordinate system P, Q, R. The similarity of both enzymes is good enough to allow the structure determination of L. caseil-lactate dehydrogenase by molecular replacement using the dogfish enzyme as a model.Sequencing results show that L. caseil-lactate dehydrogenase is lacking the N-terminal arm of vertebrate lactate dehydrogenases and electron density maps at 5 Å resolution indicate that ligands might possibly bind in the region of the missing arm. The active site loop is involved in intermolecular contacts and its structure might be different from both, apo- and ternary dogfish l-lactate dehydrogenase.     

The structure of mouse testicular lactate dehydrogenase isoenzyme C4 at 2.9 A resolution.

The structure of lactate dehydrogenase isoenzyme C4 from mouse testes was solved at 2.9 A resolution using the technique of molecular replacement. The electron density map revealed a ternary-like configuration of the flexible loop peptide although density corresponding to the coenzyme and substrate molecules was not present. Apparently the apo-lactate dehydrogenase molecule in solution is in a dynamic equilibrium between the O (loop open as found in dogfish apo-lactate dehydrogenase M4) and C (loop closed as found in a variety of ternary complexes) conformations. During crystallization of the apoenzyme one or the other conformers is selected. The apparent stability of the closed conformation for the apo-lactate dehydrogenase C4 molecule may in part explain the low catalytic turnover number of the C isoenzyme. A possible substitution of an arginine residue at position 30 may also be a contributing factor as well as allowing NADP to act as coenzyme.     

Calorimetric investigation of binding of NADH to pig muscle lactate dehydrogenase

Thermal titrations have been performed to study the enthalpy of binding (Δ H_b) of the reduced coenzyme, NADH, to the pig muscle isoenzyme (M₄) of lactate dehydrogenase (EC 1.1.1.27). It has been shown that at 25°C, pH 7.0, in 0.2 M phosphate buffer Δ H_b is ?32.5 ± 1.5 kcal per mole of enzyme. The calorimetric titration data can be well represented within the limits of experimental error by a theoretical binding curve calculated on the assumption of four independent and identical binding sites.     

A low-resolution study of testicular lactate dehydrogenase using the molecular replacement technique

The orientation of the molecular 2-fold axes of mouse testicular lactate dehydrogenase (LDHase³-C₄) was determined by a rotation function search. These were subsequently identified with the P, Q, and R axes of dogfish LDHase-M₄. Since LDHase-C₄ crystallized with one molecule in a triclinic cell, the origin of the co-ordinate system was arbitrarily fixed at the molecular center. Structure factor phases were derived from an appropriately oriented dogfish apo LDHase-M₄ phasing model and combined with the observed structure amplitudes to produce a hybrid electron density map. Density points related by the molecular 222 point symmetry were averaged so as to remove the bias of the phasing model. At 7.5 Å resolution, the structure of the crystallized mouse LDHase-C₄ was found to be without coenzyme, with a conformation indistinguishable from that of dogfish apo LDHase-M₄.     

Properties of water-insoluble matrix-bound lactate dehydrogenase.

Lactate dehydrogenase enzyme was immobilized by binding to a cyanogen bromideactivated Sepharose 4B-200 in 0.1 m phosphate buffer, pH 8.5. The immobilized enzyme was found to have lower K_m values for its substrates. K_m values for pyruvate and lactate were 8 × 10 ^?5m and 4 × 10^?3m, respectively, an order of magnitude less than the value for the native (free) enzyme. Chicken heart (H₄) lactate dehydrogenase was found to lose nearly all its substrate inhibition characteristics as a result of immobilization. The covalently bound muscle-type subunits of lactate dehydrogenase showed more favorable interaction with the muscle type than with the heart type subunits. An increase in thermal and acid stability of the dogfish muscle (M₄) lactate dehydrogenase as well as a decrease in the percentage of inhibition of enzyme activity by rabbit antisera and in the complement fixation was observed as a result of immobilization. The changes in the properties of the enzyme as a result of immobilization may be attributable to hindrance produced by the insoluble matrix as well as conformational changes in the enzyme molecules.     

35-Cl nuclear magnetic resonance studies of anion-binding sites in proteins: lactate dehydrogenase.

³⁵Cl nmr relaxation rate measurements have been used to study anion-binding sites in pig heart lactate dehydrogenase. These studies reveal two types of sites, one is intimately associated with the active site, the other is not. The nonactive site has been ascribed to a subunit site in analogy with crystallographic results from the dogfish M₄ enzyme. The binding of either the reduced or the oxidized form of NAD results in an increase in the ³⁵Cl nmr relaxation rate by a factor of 1.8–2. The enhanced nmr relaxation rate of the binary lactate dehydrogenase-NAD complex is reduced on binding of the substrate inhibitor molecules oxamate or oxalate to a value less than that exhibited by lactate dehydrogenase alone. The enhancement of the nmr relaxation rate is attributed to a decrease in the dissociation constant of Cl for the enzyme. The K_p values for Cl binding to the active center site of lactate dehydrogenase is 0.85 m and for lactate dehydrogenase-NADH is 0.25 m. The ratio of these constants, 3.4, agrees well with the measured enhancement value 3.7. The effect of coenzyme analogs on the ³⁵Cl nmr relaxation rate has been examined. 3-Acetylpyridine NAD produces an enhancement of 4.3, thionicotinamide NAD of 2.3, whereas 3-pyridinealdehyde, adenosinediphosphoribose, and adenosine diphosphate do not affect the nmr relaxation state of Cl bound to lactate dehydrogenase.     

Crystallographic study of the iron-sulfur flavoprotein trimethylamine dehydrogenase from the bacterium W3A1

Large single crystals of trimethylamine dehydrogenase, containing both [4Fe-4S]²⁺ centers and covalently bound FMN, have been prepared by the macro seeding technique. The crystals are monoclinic, space group P2₁ with cell parameters $\text{a = 147.63}\text{A}\text{?}\text{, b = 71.96}\text{A}\text{?}\text{, c = 83.66}\text{A}\text{?}\text{and}\text{β = 97.64 °}$, and diffract to at least 2.0 Å resolution. There is one dimer of approximately 166,000 M_m per asymmetric unit. A 5.0 Å resolution anomalous scattering difference Patterson has been computed which shows the presence and position of two [4Fe-4S]²⁺ centers in the asymmetric unit. A self-rotation function computed at 6.0 Å resolution indicates a non-crystallographic 2-fold axis relating the two subunits. These results show trimethylamine dehydrogenase to be composed of two identical or very similar subunits each containing one [4Fe-4S]²⁺ center.     

An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase

The three-dimensional structure of chicken triose phosphate isomerase consists of an eightfold repeat of a βα. unit. We have investigated whether there is evidence of (1) gene replication within TIMase²; and (2) a common genetic origin for TIMase and dogfish lactate dehydrogenase, another protein with a (βα)₂-β structure. Alpha carbon atoms of the βα. units and of the (βα)₂-β units were superimposed to minimise the sum of the root-mean-square distances between equivalenced atoms. Four measures of similarities between amino acids wore used in comparison of the sequences. These methods gave no definitive evidence of gene replication within TIMase. In the comparison between TIMase and lactate dehydrogenase, some three-dimensional and sequence similarities were found which can be combined to suggest that some sections of the molecules are related. However, one cannot distinguish with any certainty between convergent and divergent evolution as explanations for the apparent relationship.     

Low resolution crystal structure of hagfish insulin

Insulin from the Atlantic hagfish, Myxine glutinosa, crystallizes in space group P4₁2₁2 with a monomer in the asymmetric unit. The application of the Rossmann &; Blow (1962) rotation function, utilizing the known 2-zinc pig insulin crystal structure, has established the existence of an insulin dimer containing a crystallographic 2-fold axis. The position of the hagfish insulin molecule in the unit cell has been determined and a set of calculated phases derived. These are compared to phases found from isomorphous replacement studies. A 6 Å resolution electron density map has been calculated which shows the A and B chains are folded in a similar way to pig insulin and that the monomers are similarly organized into dimers.     

Preliminary X-ray studies on an unspecific NAD(P)H dehydrogenase from human erythrocytes

Crystals of a relatively unspecific NAD(P)H dehydrogenase from human erythrocytes suitable for X-ray analysis have been grown. They belong to space group P4₁2₁2 or its enantiomorph P4₃2₁2 with unit cell dimensions: $\text{a = b = 79.3}\text{A}\text{?}\text{and}\text{c = 38.1}\text{A}\text{?}$. The asymmetric unit contains one molecule of M_r 18,000.     

Functional anion binding sites in dogfish M4 lactate dehydrogenase

X-ray diffraction data have been collected from dogfish M₄ lactate dehydrogenase crystals in which ammonium sulfate had been exchanged by citrate at pH 6.0 and 7.8. Data were also collected from crystals which had been soaked in 0.1 m oxamate, a lactate dehydrogenase inhibitor. The difference electron density maps obtained have been interpreted in terms of two exchangeable anion binding sites, one at the active center and one between two subunits. The active center site is coincident with the substrate binding site in a ternary complex, while the subunit boundary site, which has been observed in several different forms of the enzyme, may be involved in stabilizing the tetramer.     

Peptides isolated from human liver with specific inhibitory effects on reassociation/reactivation of in vitro dissociated lactic dehydrogenase (LDH-M4 and −H4) isozymes

Two different peptides have been purified from human liver, similar to those previously reported (Schoenenberger, G.A., and Wacker, W.E.C. (1966) Biochemistry 5, 1375–1379) to be present in human urine, which may serve as metabolic regulators of lactate dehydrogenase (EC 1.1 1.27) isoenzymes (LDH-M₄ = muscle type; LDH-H₄ = heart type). By trichloroacetic acid precipitation, ultrafiltration, Sephadex G-25 and Bio-Gel P-2 columns, affinity chromatography on immobilized LDH-isozymes and HPLC two peptides which differed with respect to molecular weight, retention on the affinity columns and amino acid composition were isolated. No effect was observed when native, tetrameric lactate dehydrogenase was incubated with these peptides. However, when lactate dehydrogenase was dissociated to monomers at low pH and allowed to reassociate by adjusting the pH to 7.5 complete inhibition of the reactivation occurred when the inhibitors were incubated together with respective reassociating monomeric isozymes. The two peptides showed no cross-specificity, i.e. each peptide exhibited inhibitory activity only on one of the two isozymes LDH-M₄ or LDH-H₄. From the amino acid analyses, gel-filtration and PAGE + SDS, molecular weight of 1800 for the M₄ and ≈2700 for the H₄ inhibitor were calculated. An apparent K_i of ≈3 × 10^?5 mM for the H₄ and ≈7 × 10^?5 mM for the H₄ inhibitor was estimated. The interaction of the inhibitors with the enzyme system showed strong cooperativity with Hill coefficients of 2.9 (LDH-M₄-specific) and 2.4 (LDH-H₄-specific). Mathematical modelling of the reassociation and reactivation of lactate dehydrogenase and its specific inhibition by the peptides led to the conclusion that the peptides reacts with monomers, dimers or a transition state during the tetramerisation process. k₁ for the dimerisation step of M₄ = 2.0 × 10⁵ M^?1 · s^?1 and of H₄ = 8.2 × 10⁴ M^?1 · s^?1; k₂ for the tetramerisation step of M₄ = 2.8 × 10⁵ M^?1 · s^?1 and of H₄ = 1.2 × 10⁵ · M^?1 · s^?1, were calculated, the second step still being the faster one.     

A crystallographic investigation of citrate synthase from pig and chicken heart muscle

Citrate synthase (EC 4. 1. 3. 7.) from pig heart and chicken heart muscle can be crystallized from 10 mM phosphate buffer (pH 7. 0–7. 5) and 10–15% PEG4000 solution. The space group is P4₁2₁2 with one subunit/asymmetric unit for the pig heart enzyme. The chicken heart citrate synthase purified from Blue-dextran as well as ATP-Sepharose affinity chromatography both crystallize in space group P2₁2₁2 with one molecule/asymmetric unit, but they have different unit cell dimensions. The a-axis differs by about 17 Å between these two crystal forms, while b- and c-axis dimensions are virtually identical.     

Physical and chemical properties of lactate dehydrogenase in Homarus americanus.

Two isoenzymes of lactate dehydrogenase have been purified from Homarus americanus: One is found predominantly in the tail muscles; the other, in the walking leg muscles. This is the first demonstration of multiple forms of l-specific lactate dehydrogenase in an invertebrate organism. These proteins contain four essential sulfhydryl groups titratable by p-hydroxymercuribenzoate and 5,5′-dithiobis(2-nitrobenzoic acid). The molecular weights of these isoenzymes are dependent upon ionic strength. The native tetramer (M_r 145,000) exists in low ionic strength solutions; the active dimer (M_r 75,000), in high ionic strength solutions; this is the only example of lactate dehydrogenase disaggregation without concomitant loss in enzymatic activity. Microcomplement fixation studies suggest that there may be less than 4% difference in the primary structures of these two proteins.     

Preliminary crystallographic data for cytochromes c' of Rhodopseudomonas capsulata and Rhodospirillum molischianum.

Crystallization conditions and unit cell parameters are reported for cytochromes c′ of Rhodopseudomonas capsulata and Rhodospirillum molischianum. While both proteins naturally occur as dimers having identical subunits of M_r ~ 14,000, R. capsulata was found to crystallize in the hexagonal space group P6₂ (or its enantiomorph P6₄) with one subunit per crystallographic asymmetric unit. This result suggests that the subunits of this molecule are related by exact 2-fold symmetry.     

Crystallization and preliminary X-ray diffraction studies of leishmanolysin,the major surface metalloproteinase from Leishmania major

The membrane-bound GPI-anchored zinc metalloproteinase leishmanolysin purified from Leishmania major promastigotes has been crystallized in its mature form. Two crystal forms of leishmanolysin have been grown by the vapor diffusion method using 2-methyl-2,4-pentanediol as the precipitant. Macroseeding techniques were employed to produce large single crystals. Protein microhet-erogeneity in molecular size and charge was incorporated into both crystal forms. The tetragonal crystal form belongs to the space group P4₁2₁2 or the enantiomorph P4₃2₁2, has unit cell parameters of a = b = 63.6 Å, c = 251.4 Å, and contains one molecule per asymmetric unit. The second crystal form is monoclinic, space group C2, with unit cell dimensions a = 107.2 Å, b = 90.6 Å, c = 70.6 Å, β = 110.6°, and also contains one molecule per asymmetric unit. Both crystal forms diffract X-rays beyond 2.6 Å resolution and are suitable for X-ray analysis. Native diffraction data sets have been collected and the structure determination of leishmanolysin using a combination of the isomorphous replacement and the molecular replacement methods is in progress. © 1995 Wiley-Liss, Inc.     

Crystallization and preliminary X-ray diffraction studies of soybean agglutinin

Soybean agglutinin crystallizes in the monoclinic space group C2 with unit cell dimensions $\text{a = 118.6}\text{A}\text{?}\text{, b = 88.9}\text{A}\text{?}\text{, c = 165.9}\text{A}\text{?}\text{, β = 103.0 °}$ and one tetramer of 120,000 M_r per asymmetric unit. The crystals are suitable for high-resolution work.     

Crystallographic data of the selenoenzyme glutathione peroxidase

Glutathione peroxidase prepared from bovine erythrocytes yields small, but well-ordered plate-like crystals. X-ray investigation shows them to belong to monoclinic space group C2. Unit cell dimensions are: $\text{a = 90.4}\text{A}\text{?}\text{, b = 109.5}\text{A}\text{?}\text{, c = 58.6}\text{A}\text{?}$, β = 99 ° ± 15 min. The crystal density is ?_c = 1.36 ± 0.02 g.cm^?3. Consequently, the asymmetric unit of the crystal cell is occupied by one tetrameric molecule of M_r 84,000. Matthew's (1968) parameter Γ_M is calculated to be 1.71 ų/dalton.