Charles A. Hasemann

Structure and function of cytochromes P450:a comparative analysis of three crystal structures

BACKGROUND Cytochromes P450 catalyze the oxidation of a variety of hydrophobic substrates. Sequence identities between P450 families are generally low (10-30%), and consequently, the structure-function correlations among P450s are not clear. The crystal structures of P450terp and the hemoprotein domain of P450BM-3 were recently determined, and are compared here with the previously available structure of P450cam. RESULTS The topology of all three enzymes is quite similar. The heme-binding core structure is well conserved, except for local differences in the I helices. The greatest variation is observed in the substrate-binding regions. The structural superposition of the proteins permits an improved sequence alignment of other P450s. The charge distribution in the three structures is similarly asymmetric and defines a molecular dipole. CONCLUSIONS Based on this comparison we believe that all P450s will be found to possess the same tertiary structure. The ability to precisely predict other P450 substrate-contact residues is limited by the extreme structural heterogeneity in the substrate-recognition regions. The central I-helix structures of P450terp and P450BM-3 suggest a role for helix-associated solvent molecules as a source of catalytic protons, distinct from the mechanism for P450cam. We suggest that the P450 molecular dipole might aid in both redox-partner docking and proton recruitment for catalysis.

Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition.

MEK1 and MEK2 are closely related, dual-specificity tyrosine/threonine protein kinases found in the Ras/Raf/MEK/ERK mitogen-activated protein kinase (MAPK) signaling pathway. Approximately 30% of all human cancers have a constitutively activated MAPK pathway, and constitutive activation of MEK1 results in cellular transformation. Here we present the X-ray structures of human MEK1 and MEK2, each determined as a ternary complex with MgATP and an inhibitor to a resolution of 2.4 Å and 3.2 Å, respectively. The structures reveal that MEK1 and MEK2 each have a unique inhibitor-binding pocket adjacent to the MgATP-binding site. The presence of the potent inhibitor induces several conformational changes in the unphosphorylated MEK1 and MEK2 enzymes that lock them into a closed but catalytically inactive species. Thus, the structures reported here reveal a novel, noncompetitive mechanism for protein kinase inhibition.

Crystal structure and refinement of cytochrome P450terp at 2.3 A resolution.

Cytochrome P450terp is a class I (mitochondrial/bacterial) P450 that catalyzes the hydroxylation of alpha-terpineol as part of the catabolic assimilation of this compound by a pseudomonad species. Crystals grown from the purified protein have the symmetry of space group P6(1)22, and cell dimensions a = b = 69.4 A, c = 456.6 A, alpha = beta = 90 degrees, gamma = 120 degrees. Diffraction data were collected at the Cornell High Energy Synchrotron Source, and the structure of P450terp was solved by a combination of molecular replacement and multiple isomorphous replacement techniques. A model of P450terp was built and refined against native data, to an R-factor of 18.9% for data with I > or = sigma(I) between 6.0 A and 2.3 A resolution. This model contains 412 of the 428 P450terp amino acid residues; the loop between helices F and G is disordered in the crystal. While the overall fold of P450terp is very similar to that of P450cam, only three-quarters of the C alpha positions can be superimposed, to a root-mean-square deviation of only 1.87 A. The mode of substrate binding by P450terp can be predicted, and probable substrate contact residues identified. The heme environment and side-chain positions in the adjacent I-helix suggest possible modes of proton delivery in the catalytic cycle of the enzyme.

Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone

The crystal structure of recombinant TroA, a zinc-binding protein component of an ATP-binding cassette transport system in Treponema pallidum, was determined at a resolution of 1.8 Å. The organization of the protein is largely similar to other periplasmic ligand-binding proteins (PLBP), in that two independent globular domains interact with each other to create a zinc-binding cleft between them. The structure has one bound zinc pentavalently coordinated to residues from both domains. Unlike previous PLBP structures that have an interdomain hinge composed of β-strands, the N- and C-domains of TroA are linked by a single long backbone helix. This unique backbone helical conformation was possibly adopted to limit the hinge motion associated with ligand exchange.

The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies.

BACKGROUND Glucose homeostasis is maintained by the processes of glycolysis and gluconeogenesis. The importance of these pathways is demonstrated by the severe and life threatening effects observed in various forms of diabetes. The bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase catalyzes both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis. Thus this bifunctional enzyme plays an indirect yet key role in the regulation of glucose metabolism. RESULTS We have determined the 2.0 A crystal structure of the rat testis isozyme of this bifunctional enzyme. The enzyme is a homodimer of 55 kDa subunits arranged in a head-to-head fashion, with each monomer consisting of independent kinase and phosphatase domains. The location of ATPgammaS and inorganic phosphate in the kinase and phosphatase domains, respectively, allow us to locate and describe the active sites of both domains. CONCLUSIONS The kinase domain is clearly related to the superfamily of mononucleotide binding proteins, with a particularly close relationship to the adenylate kinases and the nucleotide-binding portion of the G proteins. This is in disagreement with the broad speculation that this domain would resemble phosphofructokinase. The phosphatase domain is structurally related to a family of proteins which includes the cofactor independent phosphoglycerate mutases and acid phosphatases.

Baculovirus expression of antibodies: A method for the expression of complete immunoglobulins in a eukaryotic host

To express complete immunoglobulin heterodimers in vitro, we have taken advantage of the baculovirus expression system. Several approaches to the simultaneous expression of recombinant heavy and light chains were examined, including coinfection with separate γ and κ expressing viruses, as well as infection with a single double recombinant virus that expresses both polypeptides. In both cases, the antibodies produced were correctly processed, glycosylated, and assembled into normal immunoglobulin heterodimers. Furthermore, the antibodies recovered from the supernatants of infected cultures behaved indistinguishably from B-cell-derived immunoglobulins with similar specificities. An additional benefit of a baculovirus-based expression system is the high yield of recombinant material produced in insect cells. Thus we describe here a general method for the high-level expression of authentic antibodies in a eukaryotic host.

The Active Sites of Fructose 6-Phosphate,2-kinase: Fructose-2,6-bisphosphatase from Rat Testis ROLES OF ASP-128, THR-52, THR-130, ASN-73, AND TYR-197

To investigate the role in catalysis and/or substrate binding of the Walker motif residues of rat testis fructose 6-phosphate,2-kinase:fructose-2,6-bisphosphatase (Fru 6-P,2-kinase:Fru-2,6-Pase), we have constructed and characterized mutant enzymes of Asp-128, Thr-52, Asn-73, Thr-130, and Tyr-197. Replacement of Asp-128 by Ala, Asn, and Ser resulted in a small decrease in Vmax and a significant increase in Km values for both substrates. These mutants exhibited similar pH activity profiles as that of the wild type enzyme. Mutation of Thr-52 to Ala resulted in an enzyme with an infinitely high Km for both substrates and an 800-fold decreased Vmax. Substitution of Asn-73 with Ala or Asp caused a 100- and 600-fold increase, respectively in KFru 6-P with only a small increase in KATP and small changes in Vmax. Mutation of Thr-130 caused small changes in the kinetic properties. Replacement of Tyr-197 with Ser resulted in an enzyme with severely decreased binding of Fru 6-P with 3-fold decreased Vmax. A fluorescent analog of ATP, 2′(3′)-O-(N-methylanthraniloyl)ATP (mant-ATP) served as a substrate with Km = 0.64 μM, and Vmax = 25 milliunits/mg and was a competitive inhibitor with respect to ATP. When mant-ATP bound to the enzyme, fluorescence intensity at 440 nm increased. mant-ATP binding of the wild type and the mutant enzymes were compared using the fluorometric method. The Kd values of the T52A and D128N enzymes were infinitely high and could not be measured, while those of the other mutant enzymes increased slightly. These results provide evidence that those amino acids are involved in substrate binding, and they are consistent with the crystallographic data. The results also suggest that Asp-128 does not serve as a nucleophile in catalysis, and since there are no other potential nucleophiles in the active site, we hypothesize that the Fru 6-P,2-kinase reaction is mediated via a transition state stabilization mechanism.

Specific cleavage of diphtheria toxin by human urokinase

Diphtheria toxin must undergo a specific cleavage reaction and subsequent reduction to express the enzymatic ADP-ribosyltransferase activity that is responsible for its toxicity. In an effort to identify potential cellular enzymes that might be involved in this process we have found that a human urinary plasminogen activator, urokinase, is capable of specifically cleaving diphtheria toxin to yield an enzymatically active A fragment (more homogeneous than that produced by trypsin cleavage) and a B fragment (with an identical amino-terminal sequence to that produced by trypsin cleavage). The results raise the possibility that urokinase or urokinase-like enzymes play a role in diphtheria toxin-mediated intoxication.

A switch in the kinase domain of rat testis 6-phosphofructo-2- kinase/fructose-2,6-bisphosphatase

The bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase plays an essential role in the regulation of glucose metabolism by both producing and degrading Fru-2,6-P(2) via its distinct catalytic activities. The 6-PF-2-K and Fru-2,6-P(2)ase active sites are located in separate domains of the enzyme. The kinase domain is structurally related to the superfamily of mononucleotide binding proteins that includes adenylate kinase and the G-proteins. We have determined three new structures of the enzymatic monomer, each with a different ligand in the ATP binding site of the 6-PF-2-K domain (AMP-PNP, PO(4), and water). A comparison of these three new structures with the ATPgammaS-bound 6-PF-2-K domain reveals a rearrangement of a helix that is dependent on the ligand bound in the ATP binding site of the enzyme. This helix motion dramatically alters the position of a catalytic residue (Lys172). This catalytic cation is analogous to the Arg residue donated by the rasGAP protein, and the Arg residue at the core of the GTP or GDP sensing switch motion seen in the heterotrimeric G-proteins. In addition, a succinate molecule is observed in the Fru-6-P binding site. Kinetic analysis of succinate inhibition of the 6-PF-2-K reaction is consistent with the structural findings, and suggests a mechanism for feedback inhibition of glycolysis by citric acid cycle intermediates. Alterations in the 6-PF-2-K kinetics of several proteins mutated near both the switch and the succinate binding site suggest a mode of communication between the ATP- and F6P binding sites. Together with these kinetic data, these new structures provide insights into the mechanism of the 6-PF-2-K activity of this important bifunctional enzyme.

Polymorphisms of immunologically relevant loci in human disease: autoimmunity and human heavy chain variable regions

In higher vertebrates there are three major groups of polymorphic molecules that are central to immunologic specificity. The genes of the major histocompatibility complex were demonstrated to be polymorphic and associated with a number of human diseases over two decades ago, and “HLA typing” is now routinely performed for several human diseases.’.’ Polymorphisms of the human T-cell receptor complex were more recently documented, and as of this writing allelic variants of T alpha, T beta, and T gamma have been described.= In several instances these variations have been associated with human Immunoglobulins are composed of heavy and light polypeptide chains; in man, allotypic forms are known within the kappa (Km) and heavy (Gm) chain families, the multiple forms of lambda being isotypic. The Gm and Km allotypes were first detected serologically, and over the years evidence has accumulated that these allotypic forms are associated with certain human diseases.’&’’ As data from other species (particularly rabbit and mouse) accumulated in which serologic markers for the variable regions could be followed in pedigree analyses with allotypes in the constant region, a paradox emerged. Although there were certain preferences for certain V regions to be associated with certain C regions, by and large there was no evidence of significant linkage disequilibrium between the variable and constant region genes.”.l4 The hypothesis developed that the described disease associations were largely related to limited amino acid variations in the constant regions of immunoglobulin molecules that somehow affected immunoglobulin function (for example, complement fixation or opsonizing capabilities). Because serologic markers in the variable region have been difficult to define in man, several investigators have turned to molecular genetic studies. Historically, human immunoglobulin V, structures have been divided into three