Paul K. Fyfe

Reaction centres: the structure and evolution of biological solar power

Reaction centres are complexes of pigment and protein that convert the electromagnetic energy of sunlight into chemical potential energy. They are found in plants, algae and a variety of bacterial species, and vary greatly in their composition and complexity. New structural information has highlighted features that are common to the different types of reaction centre and has provided insights into some of the key differences between reaction centres from different sources. New ideas have also emerged on how contemporary reaction centres might have evolved and on the possible origin of the first chlorophyll-protein complexes to harness the power of sunlight.

The purple bacterial photosynthetic unit

Now is a very exciting time for researchers in the area of the primary reactions of purple bacterial photosynthesis. Detailed structural information is now available for not only the reaction center (Lancaster et al. 1995, in: Blankenship RE et al. (eds) Anoxygenic Photosynthetic Bacteria, pp 503–526), but also LH2 from Rhodopseudomonas acidophila (McDermott et al. 1995, Nature 374: 517–521) and LH1 from Rhodospirillum rubrum (Karrasch et al. 1995. EMBO J 14: 631–638). These structures can now be integrated to produce models of the complete photosynthetic unit (PSU) (Papiz et al., 1996, Trends Plant Sci, in press), which opens the door to a much more detailed understanding of the energy transfer events occurring within the PSU.

Probing the interface between membrane proteins and membrane lipids by X-ray crystallography

Biological membranes are composed of a complex mixture of lipids and proteins, and the membrane lipids support several key biophysical functions, in addition to their obvious structural role. Recent results from X-ray crystallography are shedding new light on the precise molecular details of the protein-lipid interface.

Leishmania trypanothione synthetase-amidase structure reveals a basis for regulation of conflicting synthetic and hydrolytic activities

The bifunctional trypanothione synthetase-amidase catalyzes biosynthesis and hydrolysis of the glutathione-spermidine adduct trypanothione, the principal intracellular thiol-redox metabolite in parasitic trypanosomatids. These parasites are unique with regard to their reliance on trypanothione to determine intracellular thiol-redox balance in defense against oxidative and chemical stress and to regulate polyamine levels. Enzymes involved in trypanothione biosynthesis provide essential biological activities, and those absent from humans or for which orthologues are sufficiently distinct are attractive targets to underpin anti-parasitic drug discovery. The structure of Leishmania major trypanothione synthetase-amidase, determined in three crystal forms, reveals two catalytic domains. The N-terminal domain, a cysteine, histidine-dependent amidohydrolase/peptidase amidase, is a papain-like cysteine protease, and the C-terminal synthetase domain displays an ATP-grasp family fold common to C:N ligases. Modeling of substrates into each active site provides insight into the specificity and reactivity of this unusual enzyme, which is able to catalyze four reactions. The domain orientation is distinct from that observed in a related bacterial glutathionylspermidine synthetase. In trypanothione synthetase-amidase, the interactions formed by the C terminus, binding in and restricting access to the amidase active site, suggest that the balance of ligation and hydrolytic activity is directly influenced by the alignment of the domains with respect to each other and implicate conformational changes with amidase activity. The potential inhibitory role of the C terminus provides a mechanism to control relative levels of the critical metabolites, trypanothione, glutathionylspermidine, and spermidine in Leishmania.

Structure of Staphylococcus aureus EsxA Suggests a Contribution to Virulence by Action as a Transport Chaperone and/or Adaptor Protein

Staphylococcus aureus pathogenesis depends on a specialized protein secretion system (ESX-1) that delivers a range of virulence factors to assist infectivity. We report the characterization of two such factors, EsxA and EsxB, small acidic dimeric proteins carrying a distinctive WXG motif. EsxA crystallized in triclinic and monoclinic forms and high-resolution structures were determined. The asymmetric unit of each crystal form is a dimer. The EsxA subunit forms an elongated cylindrical structure created from side-by-side alpha-helices linked with a hairpin bend formed by the WXG motif. Approximately 25% of the solvent accessible surface area of each subunit is involved in interactions, predominantly hydrophobic, with the partner subunit. Secondary-structure predictions suggest that EsxB displays a similar structure. The WXG motif helps to create a shallow cleft at each end of the dimer, forming a short beta-sheet-like feature with an N-terminal segment of the partner subunit. Structural and sequence comparisons, exploiting biological data on related proteins found in Mycobacterium tuberculosis, suggest that this family of proteins may contribute to pathogenesis by transporting protein cargo through the ESX-1 system exploiting a C-terminal secretion signal and/or are capable of acting as adaptor proteins to facilitate interactions with host receptor proteins.

Is There a Conserved Interaction between Cardiolipin and the Type II Bacterial Reaction Center

In a recent publication, the structural details of an interaction between the Rhodobacter sphaeroides reaction center and the anionic phospholipid diphosphatidyl glycerol (cardiolipin) were described (K. E. McAuley, P. K. Fyfe, J. P. Ridge, N. W. Isaacs, R. J. Cogdell, and M. R. Jones, 1999, Proc. Natl. Acad. Sci. U.S.A. 96:14706-14711). This was the first crystallographic description of an interaction between this biologically important lipid and an integral membrane protein and was also the first piece of evidence that the reaction center has a specific interaction with cardiolipin. We have examined the extent to which the residues that interact with the cardiolipin are conserved in other species of photosynthetic bacteria with this type of reaction center and discuss the possibility that this cardiolipin binding site is a conserved feature of these reaction centers. We look at how sequence variations that would affect the shape of the cardiolipin binding site might affect the protein-cardiolipin interaction, by modeling the binding of cardiolipin to the reaction center from Rhodopseudomonas viridis.

Specificity and Mechanism of Acinetobacter baumanii Nicotinamidase: Implications for Activation of the Front‐Line Tuberculosis Drug Pyrazinamide

Nicotinamidase (EC 3.5.1.19) catalyzes hydrolysis of nicotinamide to nicotinic acid and ammonia, an important reaction in the NAD salvage pathway. This activity has a fortuitous medical benefit since the Mycobacterium tuberculosis enzyme converts the nicotinamide analogue prodrug pyrazinamide into the bacteriostatic pyrazinoic acid, hence the alternative name, pyrazinamidase (PncA). Pyrazinoic acid inhibits M. tuberculosis type I fatty acid synthase, represses mycolic acid biosynthesis, and appears to affect membrane energetics and acidification of the cytoplasm. It is active against semidormant tubercle bacilli and with rifampicin and isoniazid, forms the front-line tuberculosis treatment. 3] Though studies of PncA have revealed aspects of its structure and biochemical activity there are no structural data on how the enzyme binds and processes physiological ligands. Highresolution crystal structures of Acinetobacter baumanii PncA (AbPncA) complexed with nicotinic acid and pyrazinoic acid now provide direct evidence for the interactions that govern the specificity and mechanism, and of how a valued antibacterial agent is activated. Recombinant AbPncA was prepared, the dimeric, colorless enzyme was purified in high yield and its kinetic properties determined. With pyrazinamide as the substrate the following values were obtained; KM = 106.9 mm, Vmax = 62.8 nmol min , kcat. = 3.1 min , specific activity 132 mmmin 1 mg . These values are comparable to literature values, for example, the specific activity of M. tuberculosis PncA (MtPncA) with pyrazinamide is 82 mmmin 1 mg . Two crystal forms (I and II) were obtained with nicotinic and pyrazinoic acid, respectively, and the structures determined. PncA is a divalent cation-dependent enzyme and activity has been reported with Fe, Mn, and Zn ions. As expected, metal ions were observed in the structures. Inductively coupled plasma-atomic emission spectrometry (ICP-OES) identified that recombinant AbPncA contained Fe and Zn ions in an approximate 1:1 ratio with a trace of Mn present. However, anomalous dispersion measurements are consistent with a higher occupancy of Zn at the active site and the crystallographic models contain that cation. We refer to Zn ions in discussion but judge it likely that AbPncA functions in the presence of different divalent cations. (Experimental details, including enzyme activity and metal-ion identification, together with sequence alignments, and additional figures are given as Supporting Information Figure S1–S8). Crystals were obtained in the presence of cacodylate buffer and form II shows dimethylarsinoyl-modified Cys159 in the active site, an artifact of crystallization (Supporting Information, Figure S1, S2). The steric hindrance of this modification precludes full occupancy of pyrazinoic acid such that the final refinement was performed with occupancy 0.8 for pyrazinoic acid, 0.2 for the modified cysteine. Crystal form I has two molecules, form II a single molecule in the asymmetric unit, respectively, with a root-mean-square deviation (r.m.s.d.) derived from least-squares fit of Ca atoms of these three molecules of 0.2 . The structures and the interactions formed by ligands within the active sites are essentially identical and we concentrate on form I, a 1.65 resolution structure with full occupancy ligand (Supporting Information, Figure S3). About 60% of residues form elements of secondary structure, these are eight a-helices and nine b-strands (Figure 1, and Supporting Information, Figure S4). The core of the subunit is a parallel b-sheet of strands 1, 2, 5–9. Three helices (a5, a6, a7) lie on one side of the sheet, with a2 placed against the other. A subdomain is placed at

Structure and reactivity of Trypanosoma brucei pteridine reductase: inhibition by the archetypal antifolate methotrexate

The protozoan Trypanosoma brucei has a functional pteridine reductase (TbPTR1), an NADPH‐dependent short‐chain reductase that participates in the salvage of pterins, which are essential for parasite growth. PTR1 displays broad‐spectrum activity with pterins and folates, provides a metabolic bypass for inhibition of the trypanosomatid dihydrofolate reductase and therefore compromises the use of antifolates for treatment of trypanosomiasis. Catalytic properties of recombinant TbPTR1 and inhibition by the archetypal antifolate methotrexate have been characterized and the crystal structure of the ternary complex with cofactor NADP+ and the inhibitor determined at 2.2 Å resolution. This enzyme shares 50% amino acid sequence identity with Leishmania major PTR1 (LmPTR1) and comparisons show that the architecture of the cofactor binding site, and the catalytic centre are highly conserved, as are most interactions with the inhibitor. However, specific amino acid differences, in particular the placement of Trp221 at the side of the active site, and adjustment of the β6‐α6 loop and α6 helix at one side of the substrate‐binding cleft significantly reduce the size of the substrate binding site of TbPTR1 and alter the chemical properties compared with LmPTR1. A reactive Cys168, within the active site cleft, in conjunction with the C‐terminus carboxyl group and His267 of a partner subunit forms a triad similar to the catalytic component of cysteine proteases. TbPTR1 therefore offers novel structural features to exploit in the search for inhibitors of therapeutic value against African trypanosomiasis.

Protein-lipid interactions in the purple bacterial reaction centre

The purple bacterial reaction centre uses the energy of sunlight to power energy-requiring reactions such as the synthesis of ATP. During the last 20 years, a combination of X-ray crystallography, spectroscopy and mutagenesis has provided a detailed insight into the mechanism of light energy transduction in the bacterial reaction centre. In recent years, structural techniques including X-ray crystallography and neutron scattering have also been used to examine the environment of the reaction centre. This mini-review focuses on recent studies of the surface of the reaction centre, and briefly discusses the importance of the specific protein-lipid interactions that have been resolved for integral membrane proteins.

Tuning of the optical and electrochemical properties of the primary donor bacteriochlorophylls in the reaction centre from Rhodobacter sphaeroides: spectroscopy and structure.

A series of mutations have been introduced at residue 168 of the L-subunit of the reaction centre from Rhodobacter sphaeroides. In the wild-type reaction centre, residue His L168 donates a strong hydrogen bond to the acetyl carbonyl group of one of the pair of bacteriochlorophylls (BChl) that constitutes the primary donor of electrons. Mutation of His L168 to Phe or Leu causes a large decrease in the mid-point redox potential of the primary electron donor, consistent with removal of this strong hydrogen bond. Mutations to Lys, Asp and Arg cause smaller decreases in redox potential, indicative of the presence of weak hydrogen bond and/or an electrostatic effect of the polar residue. A spectroscopic analysis of the mutant complexes suggests that replacement of the wild-type His residue causes a decrease in the strength of the coupling between the two primary donor bacteriochlorophylls. The X-ray crystal structure of the mutant in which His L168 has been replaced by Phe (HL168F) was determined to a resolution of 2.5 A, and the structural model of the HL168F mutant was compared with that of the wild-type complex. The mutation causes a shift in the position of the primary donor bacteriochlorophyll that is adjacent to residue L168, and also affects the conformation of the acetyl carbonyl group of this bacteriochlorophyll. This conformational change constitutes an approximately 27 degrees through-plane rotation, rather than the large into-plane rotation that has been widely discussed in the context of the HL168F mutation. The possible structural basis of the altered spectroscopic properties of the HL168F mutant reaction centre is discussed, as is the relevance of the X-ray crystal structure of the HL168F mutant to the possible structures of the remaining mutant complexes.