Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds

Engineering neuroglobin nitrite reductase activity based on myoglobin models

Neuroglobin is a hemoprotein expressed in several nervous system cell lineages with yet unknown physiological functions. Neuroglobin presents a very similar structure to that of the related globins hemoglobin and myoglobin, but shows an hexacoordinate heme as compared to the pentacoordinated heme of myoglobin and hemoglobin. While several reactions of neuroglobin have been characterized in vitro, the relative importance of most of those reactions in vivo is yet undefined. Neuroglobin, like other heme proteins, can reduce nitrite to nitric oxide, providing a possible route to generate nitric oxide in vivo in low oxygen conditions. The reaction kinetics are highly dependent on the nature of the distal residue, and replacement of the distal histidine His64(E7) can increase the reaction rate constants by several orders of magnitude. However, mutation of other distal pocket positions such as Phe28(B10) or Val68(E11) has more limited impact on the rates. Computational analysis using myoglobin as template, guided by the structure of dedicated nitrite reductases like cytochrome cd1 nitrite reductase, has pointed out that combined mutations of the residues B10 and CD1 could increase the nitrite reductase activity of myoglobin, by mimicking the environment of the distal heme pocket in cytochrome cd1 nitrite reductase. As neuroglobin shows high sequence and structural homology with myoglobin, we hypothesized that such mutations (F28H and F42Y in neuroglobin) could also modify the nitrite reductase activity of neuroglobin. Here we study the effect of these mutations. Unfortunately, we do not observe in any case an increase in the nitrite reduction rates. Our results provide some further indications of nitrite reductase regulation in neuroglobin and highlight the minor but critical differences between the structure of penta- and hexacoordinate globins.

Efficacy of simultaneous hexavalent chromium biosorption and nitrogen removal by the aerobic denitrifying bacterium Pseudomonas stutzeri YC-34 from chromium-rich wastewater

The impact of high concentrations of heavy metals and the loss of functional microorganisms usually affect the nitrogen removal process in wastewater treatment systems. In the study, a unique auto-aggregating aerobic denitrifier (Pseudomonas stutzeri strain YC-34) was isolated with potential applications for Cr(VI) biosorption and reduction. The nitrogen removal efficiency and denitrification pathway of the strain were determined by measuring the concentration changes of inorganic nitrogen during the culture of the strain and amplifying key denitrification functional genes. The changes in auto-aggregation index, hydrophobicity index, and extracellular polymeric substances (EPS) characteristic index were used to evaluate the auto-aggregation capacity of the strain. Further studies on the biosorption ability and mechanism of cadmium in the process of denitrification were carried out. The changes in tolerance and adsorption index of cadmium were measured and the micro-characteristic changes on the cell surface were analyzed. The strain exhibited excellent denitrification ability, achieving 90.58% nitrogen removal efficiency with 54 mg/L nitrate-nitrogen as the initial nitrogen source and no accumulation of ammonia and nitrite-nitrogen. Thirty percentage of the initial nitrate-nitrogen was converted to N₂, and only a small amount of N₂O was produced. The successful amplification of the denitrification functional genes, norS, norB, norR, and nosZ, further suggested a complete denitrification pathway from nitrate to nitrogen. Furthermore, the strain showed efficient aggregation capacity, with the auto-aggregation and hydrophobicity indices reaching 78.4 and 75.5%, respectively. A large amount of protein-containing EPS was produced. In addition, the strain effectively removed 48.75, 46.67, 44.53, and 39.84% of Cr(VI) with the initial concentrations of 3, 5, 7, and 10 mg/L, respectively, from the nitrogen-containing synthetic wastewater. It also could reduce Cr(VI) to the less toxic Cr(III). FTIR measurements and characteristic peak deconvolution analysis demonstrated that the strain had a robust hydrogen-bonded structure with strong intermolecular forces under the stress of high Cr(VI) concentrations. The current results confirm that the novel denitrifier can simultaneously remove nitrogen and chromium and has potential applications in advanced wastewater treatment for the removal of multiple pollutants from sewage.

Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis

Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.

A critical review of aerobic denitrification: Insights into the intracellular electron transfer

Aerobic denitrification is a novel biological nitrogen removal technology, which has been widely investigated as an alternative to the conventional denitrification and for its unique advantages. To fully comprehend aerobic denitrification, it is essential to clarify the regulatory mechanisms of intracellular electron transfer during aerobic denitrification. However, reports on intracellular electron transfer during aerobic denitrification are rather limited. Thus, the purpose of this review is to discuss the molecular mechanism of aerobic denitrification from the perspective of electron transfer, by summarizing the advancements in current research on electron transfer based on conventional denitrification. Firstly, the implication of aerobic denitrification is briefly discussed, and the status of current research on aerobic denitrification is summarized. Then, the occurring foundation and significance of aerobic denitrification are discussed based on a brief review of the key components involved in the electron transfer of denitrifying enzymes. Moreover, a strategy for enhancing the efficiency of aerobic denitrification is proposed on the basis of the regulatory mechanisms of denitrification enzymes. Finally, scientific outlooks are given for further investigation on aerobic denitrification in the future. This review could help clarify the mechanism of aerobic denitrification from the perspective of electron transfer.

Characterization of an l-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations

l-Ascorbate (vitamin C) is ubiquitous in both our diet and the environment. Here we report that Ralstonia eutropha H16 (Cupriavidus necator ATCC 17699) uses l-ascorbate as sole carbon source via a novel catabolic pathway. RNaseq identified eight candidate catabolic genes, sequence similarity networks, and genome neighborhood networks guided predictions for function of the encoded proteins, and the predictions were confirmed by in vitro assays and in vivo growth phenotypes of gene deletion mutants. l-Ascorbate, a lactone, is oxidized and ring-opened by enzymes in the cytochrome b₅₆₁ and gluconolactonase families, respectively, to form 2,3-diketo-l-gulonate. A protein predicted to have a WD40-like fold catalyzes an unprecedented benzilic acid rearrangement involving migration of a carboxylate group to form 2-carboxy-l-lyxonolactone; the lactone is hydrolyzed by a member of the amidohydrolase superfamily to yield 2-carboxy-l-lyxonate. A member of the PdxA family of oxidative decarboxylases catalyzes a novel decarboxylation that uses NAD⁺ catalytically. The product, l-lyxonate, is catabolized to α-ketoglutarate by a previously characterized pathway. The pathway is found in hundreds of bacteria, including the pathogens Pseudomonas aeruginosa and Acinetobacter baumannii.

Simultaneous nitrification and denitrification by a novel isolated Pseudomonas sp. JQ-H3 using polycaprolactone as carbon source

The novel isolated strain JQ-H3 exhibited heterotrophic nitrification-aerobic denitrification (HN-AD) ability using poly (ε-caprolactone) (PCL) as a sole carbon source under aerobic conditions. This was the first time that a PCL-degrading bacterium was characterized to be with capability of nitrifying and denitrifying performances. Strain JQ-H3 removed approximately 95.40% of NH₄⁺-N (102.40 mg/L), about 91.1% of NO₃^--N (99.01 mg/L), with the maximum specific removal rates of 0.308 mg NH₄⁺-N/mg DCW/h and 0.220 mg NO₃^--N/mg DCW/h, respectively. The functional genes amoA, napA, nirS, cnorB, and nosZ were successfully expressed during the nitrogen removal process. An increasing PCL concentrations caused a decline in cell growth and nitrogen removal efficiency, which was attributed to the decrease in the rate of the PCL hydrolysis and the amount of dissolved organic carbon (DOC) release. These results demonstrated the strain as an ideal candidate for nitrogen removal from wastewater by using PCL as carbon source.

Complexome analysis of the nitrite-dependent methanotroph Methylomirabilis lanthanidiphila

The atmospheric concentration of the potent greenhouse gases methane and nitrous oxide (N₂O) has increased drastically during the last century. Methylomirabilis bacteria can play an important role in controlling the emission of these two gases from natural ecosystems, by oxidizing methane to CO₂ and reducing nitrite to N₂ without producing N₂O. These bacteria have an anaerobic metabolism, but are proposed to possess an oxygen-dependent pathway for methane activation. Methylomirabilis bacteria reduce nitrite to NO, and are proposed to dismutate NO into O₂ and N₂ by a putative NO dismutase (NO-D). The O₂ produced in the cell can then be used to activate methane by a particulate methane monooxygenase. So far, the metabolic model of Methylomirabilis bacteria was based mainly on (meta)genomics and physiological experiments. Here we applied a complexome profiling approach to determine which of the proposed enzymes are actually expressed in Methylomirabilis lanthanidiphila. To validate the proposed metabolic model, we focused on enzymes involved in respiration, as well as nitrogen and carbon transformation. All complexes suggested to be involved in nitrite-dependent methane oxidation, were identified in M. lanthanidiphila, including the putative NO-D. Furthermore, several complexes involved in nitrate reduction/nitrite oxidation and NO reduction were detected, which likely play a role in detoxification and redox homeostasis. In conclusion, complexome profiling validated the expression and composition of enzymes hypothesized to be involved in the energy, methane and nitrogen metabolism of M. lanthanidiphila, thereby further corroborating their unique metabolism involved in the environmentally relevant process of nitrite-dependent methane oxidation.

Characterization of an aerobic denitrifier Pseudomonas stutzeri strain XL-2 to achieve efficient nitrate removal

An aerobic denitrifier was newly isolated and identified as Pseudomonas stutzeri strain XL-2. Strain XL-2 removed 97.9% of nitrate with an initial concentration about 100 mg/L. Nitrogen balance indicates that 12.4% of the initial nitrogen was converted to N₂O, and 62.4% was converted to N₂. Single factor experiments indicate that the optimal conditions for nitrate removal were C/N ratio of 10, temperature of 30 °C and shaking speed of 120 rpm. Sequence amplification indicates that the denitrification genes of napA, nirS, norB and nosZ were present in strain XL-2. Combined with nitrogen balance, strain XL-2 presents the metabolic pathway of NO₃^- → NO₂^- → NO  →  N₂O → N₂ under aerobic conditions. The expression of napA and nirS might be responsible for the tolerance of dissolved oxygen by strain XL-2 during denitrification process.

Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.

Conformational Dynamics, Ligand Binding and Effects of Mutations in NirE an S-Adenosyl-L-Methionine Dependent Methyltransferase

Heme d1, a vital tetrapyrrol involved in the denitrification processes is synthesized from its precursor molecule precorrin-2 in a chemical reaction catalysed by an S-adenosyl-L-methionine (SAM) dependent Methyltransferase (NirE). The NirE enzyme catalyses the transfer of a methyl group from the SAM to uroporphyrinogen III and serves as a novel potential drug target for the pharmaceutical industry. An important insight into the structure-activity relationships of NirE has been revealed by elucidating its crystal structure, but there is still no understanding about how conformational flexibility influences structure, cofactor and substrate binding by the enzyme as well as the structural effects of mutations of residues involved in binding and catalysis. In order to provide this missing but very important information we performed a comprehensive atomistic molecular dynamics study which revealed that i) the binding of the substrate contributes to the stabilization of the structure of the full complex; ii) conformational changes influence the orientation of the pyrrole rings in the substrate, iii) more open conformation of enzyme active site to accommodate the substrate as an outcome of conformational motions; and iv) the mutations of binding and active site residues lead to sensitive structural changes which influence binding and catalysis.

A phylogenetic approach to study the origin and evolution of the CRINKLY4 family

Cell-cell communication plays a crucial role in plant growth and development and relies to a large extent on peptide ligand-receptor kinase signaling mechanisms. The CRINKLY4 (CR4) family of receptor-like kinases is involved in a wide range of developmental processes in plants, including mediating columella stem cell identity and differentiation in the Arabidopsis thaliana root tip. Members of the CR4 family contain a signal peptide, an extracellular part, a single-pass transmembrane helix and an intracellular cytoplasmic protein kinase domain. The main distinguishing features of the family are the presence of seven "crinkly" repeats and a TUMOR NECROSIS FACTOR RECEPTOR (TNFR)-like domain in the extracellular part. Here, we investigated the evolutionary origin of the CR4 family and explored to what extent members of this family are conserved throughout the green lineage. We identified members of the CR4 family in various dicots and monocots, and also in the lycophyte Selaginella moellendorffii and the bryophyte Physcomitrella patens. In addition, we attempted to gain insight in the evolutionary origin of different CR4-specific domains, and we could detect "crinkly" repeat containing proteins already in single celled algae. Finally, we related the presence of likely functional CR4 orthologs to its best described signaling module comprising CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 40 (CLE40), WUSCHEL RELATED HOMEOBOX 5 (WOX5), CLAVATA 1 (CLV1), and ARABIDOPSIS CR4 (ACR4), and established that this module likely is already present in bryophytes and lycophytes.

Crystal structure of a plant albumin from Cicer arietinum (chickpea) possessing hemopexin fold and hemagglutination activity

Crystal structure of a reported PA2 albumin from Cicer arietinum shows that it belongs to hemopexin fold family, has four beta-propeller motifs and possesses hemagglutination activity, making it different from known legume lectins. A plant albumin (PA2) from Cicer arietinum, presumably a lectin (CAL) owing to its hemagglutination activity which is inhibited by complex sugars as well as glycoproteins such as fetuin, desialylated fetuin and fibrinogen. The three-dimensional structure of this homodimeric protein has been determined using X-ray crystallography at 2.2 Å in two crystal forms: orthorhombic (P21212) and trigonal (P3). The structure determined using molecular replacement method and refined in orthorhombic crystal form reached R-factors R free 22.6 % and R work 18.2 % and in trigonal form had 22.3 and 17.9 % in the resolution range of 20.0-2.2 and 35.3-2.2 Å, respectively. Interestingly, unlike the known legume lectin fold, the structure of this homodimeric hemagglutinin belonged to hemopexin fold that consisted of four-bladed β-propeller architecture. Each subunit has a central cavity forming a channel, inside of which is lined with hydrophobic residues. The channel also bears binding sites for ligands such as calcium, sodium and chloride ions, iodine atom in the case of iodine derivative and water molecules. However, none of these ligands seem important for the sugar recognition. No monosaccharide sugar specificity could be detected using hemagglutination inhibition. Chemical modification studies identified a potential sugar-binding site per subunit molecule. Comparison of C-alpha atom positions in subunit structures showed that the deviations between the two crystal forms were more with respect to blades I and IV. Differences also existed between subunits in two forms in terms of type and site of ligand binding.

The evolution of respiratory O2/NO reductases: an out-of-the-phylogenetic-box perspective

Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O2-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O2 in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O2-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O2-levels on life is the evolutionary history of the enzyme allowing organisms to tap into the redox power of molecular oxygen, i.e. the bioenergetic O2 reductases, alias the cytochrome and quinol oxidases. Consequently, molecular phylogenies reconstructed for this enzyme superfamily have been exploited over the last two decades in attempts to elucidate the interlocking between O2 levels in the environment and the evolution of respiratory bioenergetic processes. Although based on strictly identical datasets, these phylogenetic approaches have led to diametrically opposite scenarios with respect to the history of both the enzyme superfamily and molecular oxygen on the Earth. In an effort to overcome the deadlock of molecular phylogeny, we here review presently available structural, functional, palaeogeochemical and thermodynamic information pertinent to the evolution of the superfamily (which notably also encompasses the subfamily of nitric oxide reductases). The scenario which, in our eyes, most closely fits the ensemble of these non-phylogenetic data, sees the low O2-affinity SoxM- (or A-) type enzymes as the most recent evolutionary innovation and the high-affinity O2 reductases (SoxB or B and cbb3 or C) as arising independently from NO-reducing precursor enzymes.

Parasite prolyl oligopeptidases and the challenge of designing chemotherapeuticals for Chagas disease, leishmaniasis and African trypanosomiasis

The trypanosomatids Trypanosoma cruzi, Leishmania spp. and Trypanosoma brucei spp. cause Chagas disease, leishmaniasis and human African trypanosomiasis, respectively. It is estimated that over 10 million people worldwide suffer from these neglected diseases, posing enormous social and economic problems in endemic areas. There are no vaccines to prevent these infections and chemotherapies are not adequate. This picture indicates that new chemotherapeutic agents must be developed to treat these illnesses. For this purpose, understanding the biology of the pathogenic trypanosomatid-host cell interface is fundamental for molecular and functional characterization of virulence factors that may be used as targets for the development of inhibitors to be used for effective chemotherapy. In this context, it is well known that proteases have crucial functions for both metabolism and infectivity of pathogens and are thus potential drug targets. In this regard, prolyl oligopeptidase and oligopeptidase B, both members of the S9 serine protease family, have been shown to play important roles in the interactions of pathogenic protozoa with their mammalian hosts and may thus be considered targets for drug design. This review aims to discuss structural and functional properties of these intriguing enzymes and their potential as targets for the development of drugs against Chagas disease, leishmaniasis and African trypanosomiasis.

Quinone-dependent alcohol dehydrogenases and FAD-dependent alcohol oxidases

This review considers quinone-dependent alcohol dehydrogenases and FAD-dependent alcohol oxidases, enzymes that are present in numerous methylotrophic eu- and prokaryotes and significantly differ in their primary and quaternary structure. The cofactors of the enzymes are bound to the protein polypeptide chain through ionic and hydrophobic interactions. Microorganisms containing these enzymes are described. Methods for purification of the enzymes, their physicochemical properties, and spatial structures are considered. The supposed mechanism of action and practical application of these enzymes as well as their producers are discussed.

Multi-heme proteins: nature's electronic multi-purpose tool

While iron is often a limiting nutrient to Biology, when the element is found in the form of heme cofactors (iron protoporphyrin IX), living systems have excelled at modifying and tailoring the chemistry of the metal. In the context of proteins and enzymes, heme cofactors are increasingly found in stoichiometries greater than one, where a single protein macromolecule contains more than one heme unit. When paired or coupled together, these protein associated heme groups perform a wide variety of tasks, such as redox communication, long range electron transfer and storage of reducing/oxidizing equivalents. Here, we review recent advances in the field of multi-heme proteins, focusing on emergent properties of these complex redox proteins, and strategies found in Nature where such proteins appear to be modular and essential components of larger biochemical pathways. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.

Up, down, and around: identifying recurrent interactions within and between super-secondary structures in β-propellers

The examination and analysis of super-secondary structures or other specific structural patterns associated with particular functions, sequence motifs, or structural contexts require that the set of structures examined shares the same feature. This seems obvious but in practice this may often present problems such as identifying complete sets of data avoiding false positives. In the case of the β-propeller structures the symmetry of the propeller creates problems for many structure similarity search programs. Here we present a procedure that will identify propeller structures in PDB and assign them to the different N-propeller types. In addition we outline methods to examine similarities and differences within and between the four stranded up-and-down blades of the β-propeller.

How to make a living from anaerobic ammonium oxidation

Anaerobic ammonium-oxidizing (anammox) bacteria primarily grow by the oxidation of ammonium coupled to nitrite reduction, using CO2 as the sole carbon source. Although they were neglected for a long time, anammox bacteria are encountered in an enormous species (micro)diversity in virtually any anoxic environment that contains fixed nitrogen. It has even been estimated that about 50% of all nitrogen gas released into the atmosphere is made by these 'impossible' bacteria. Anammox catabolism most likely resides in a special cell organelle, the anammoxosome, which is surrounded by highly unusual ladder-like (ladderane) lipids. Ammonium oxidation and nitrite reduction proceed in a cyclic electron flow through two intermediates, hydrazine and nitric oxide, resulting in the generation of proton-motive force for ATP synthesis. Reduction reactions associated with CO2 fixation drain electrons from this cycle, and they are replenished by the oxidation of nitrite to nitrate. Besides ammonium or nitrite, anammox bacteria use a broad range of organic and inorganic compounds as electron donors. An analysis of the metabolic opportunities even suggests alternative chemolithotrophic lifestyles that are independent of these compounds. We note that current concepts are still largely hypothetical and put forward the most intriguing questions that need experimental answers.

The Dos family of globin-related sensors using PAS domains to accommodate haem acting as the active site for sensing external signals

Sensor proteins play crucial roles in maintaining homeostasis of cells by sensing changes in extra- and intracellular chemical and physical conditions to trigger biological responses. It has recently become clear that gas molecules function as signalling molecules in these biological regulatory systems responsible for transcription, chemotaxis, synthesis/hydrolysis of nucleotide second messengers, and other complex physiological processes. Haem-containing sensor proteins are widely used to sense gas molecules because haem can bind gas molecules reversibly. Ligand binding to the haem in the sensor proteins triggers conformational changes around the haem, which results in their functional regulation. Spectroscopic and crystallographic studies are essential to understand how these sensor proteins function in these biological regulatory systems. In this chapter, I discuss structural and functional relationships of haem-containing PAS and PAS-related families of the sensor proteins.

Structure of the RACK1 dimer from Saccharomyces cerevisiae

Receptor for activated C-kinase 1 (RACK1) serves as a scaffolding protein in numerous signaling pathways involving kinases and membrane-bound receptors from different cellular compartments. It exists simultaneously as a cytosolic free form and as a ribosome-bound protein. As part of the 40S ribosomal subunit, it triggers translational regulation by establishing a direct link between protein kinase C and the protein synthesis machinery. It has been suggested that RACK1 could recruit other signaling molecules onto the ribosome, providing a signal-specific modulation of the translational process. RACK1 is able to dimerize both in vitro and in vivo. This homodimer formation has been observed in several processes including the regulation of the N-methyl-d-aspartate receptor by the Fyn kinase in the brain and the oxygen-independent degradation of hypoxia-inducible factor 1. The functional relevance of this dimerization is, however, still unclear and the question of a possible dimerization of the ribosome-bound protein is still pending. Here, we report the first structure of a RACK1 homodimer, as determined from two independent crystal forms of the Saccharomyces cerevisiae RACK1 protein (also known as Asc1p) at 2.9 and 3.9 Å resolution. The structure reveals an atypical mode of dimerization where monomers intertwine on blade 4, thus exposing a novel surface of the protein to potential interacting partners. We discuss the significance of the dimer structure for RACK1 function.

An alternative view of the proposed alternative activities of hemopexin

Hemopexin is a plasma protein that plays a well-established biological role in sequestering heme that is released into the plasma from hemoglobin and myoglobin as the result of intravascular or extravascular hemolysis as well as from skeletal muscle trauma or neuromuscular disease. In recent years, a variety of additional biological activities have been attributed to hemopexin, for example, hyaluronidase activity, serine protease activity, pro-inflammatory and anti-inflammatory activity as well as suppression of lymphocyte necrosis, inhibition of cellular adhesion, and binding of divalent metal ions. This review examines the challenges involved in the purification of hemopexin from plasma and in the recombinant expression of hemopexin and evaluates the questions that these challenges and the characteristics of hemopexin raise concerning the validity of many of the new activities proposed for this protein. As well, an homology model of the three-dimensional structure of human hemopexin is used to reveal that the protein lacks the catalytic triad that is characteristic of many serine proteases but that hemopexin possesses two highly exposed Arg-Gly-Glu sequences that may promote interaction with cell surfaces.

Crystal structure of Leishmania major oligopeptidase B gives insight into the enzymatic properties of a trypanosomatid virulence factor

Oligopeptidase B (OPB) is a serine peptidase with dibasic substrate specificity. It is found in bacteria, plants, and trypanosomatid pathogens, where it has been identified as a virulence factor and potential drug target. In this study we expressed active recombinant Leishmania major OPB and provide the first structure of an oligopeptidase B at high resolution. The crystallographic study reveals that OPB comprises two domains, a catalytic and a propeller domain, linked together by a hinge region. The structure has been determined in complex with the oligopeptide, protease-inhibitor antipain, giving detailed information on the enzyme active site and extended substrate binding pockets. It shows that Glu-621 plays a critical role in the S1 binding pocket and, along with Phe-603, is largely responsible for the enzyme substrate specificity in P1. In the S2 binding pocket, Tyr-499 was shown to be important for substrate stability. The structure also allowed an investigation into the function of residues highlighted in other studies including Glu-623, which was predicted to be involved in the S1 binding pocket but is found forming an inter-domain hydrogen bond. Additional important salt bridges/hydrogen bonds between the two domains were observed, highlighting the significance of the domain interface in OPB. This work provides a foundation for the study of the role of OPBs as virulence factors in trypanosomatids. It could facilitate the development of specific OPB inhibitors with therapeutic potential by exploiting its unique substrate recognition properties as well as providing a model for OPBs in general.

New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases

Endo-1,5-α-L-arabinanases are glycosyl hydrolases that are able to cleave the glycosidic bonds of α-1,5-L-arabinan, releasing arabino-oligosaccharides and L-arabinose. Two extracellular endo-1,5-α-L-arabinanases have been isolated from Bacillus subtilis, BsArb43A and BsArb43B (formally named AbnA and Abn2, respectively). BsArb43B shows low sequence identity with previously characterized 1,5-α-L-arabinanases and is a much larger enzyme. Here we describe the 3D structure of native BsArb43B, biochemical and structure characterization of two BsArb43B mutant proteins (H318A and D171A), and the 3D structure of the BsArb43B D171A mutant enzyme in complex with arabinohexose. The 3D structure of BsArb43B is different from that of other structurally characterized endo-1,5-α-L-arabinanases, as it comprises two domains, an N-terminal catalytic domain, with a 3D fold similar to that observed for other endo-1,5-α-L-arabinanases, and an additional C-terminal domain. Moreover, this work also provides experimental evidence for the presence of a cluster containing a calcium ion in the catalytic domain, and the importance of this calcium ion in the enzymatic mechanism of BsArb43B.

Molecular, functional and structural properties of the prolyl oligopeptidase of Trypanosoma cruzi (POP Tc80), which is required for parasite entry into mammalian cells

We have demonstrated that the 80 kDa POP Tc80 (prolyl oligopeptidase of Trypanosoma cruzi) is involved in the process of cell invasion, since specific inhibitors block parasite entry into non-phagocytic mammalian host cells. In contrast with other POPs, POP Tc80 is capable of hydrolysing large substrates, such as fibronectin and native collagen. In this study, we present the cloning of the POPTc80 gene, whose deduced amino acid sequence shares considerable identity with other members of the POP family, mainly within its C-terminal portion that forms the catalytic domain. Southern-blot analysis indicated that POPTc80 is present as a single copy in the genome of the parasite. These results are consistent with mapping of POPTc80 to a single chromosome. The active recombinant protein (rPOP Tc80) displayed kinetic properties comparable with those of the native enzyme. Novel inhibitors were assayed with rPOP Tc80, and the most efficient ones presented values of inhibition coefficient Ki < or = 1.52 nM. Infective parasites treated with these specific POP Tc80 inhibitors attached to the surface of mammalian host cells, but were incapable of infecting them. Structural modelling of POP Tc80, based on the crystallized porcine POP, suggested that POP Tc80 is composed of an alpha/beta-hydrolase domain containing the catalytic triad Ser548-Asp631-His667 and a seven-bladed beta-propeller non-catalytic domain. Docking analysis suggests that triple-helical collagen access to the catalytic site of POP Tc80 occurs in the vicinity of the interface between the two domains.

Demonstration of proton-coupled electron transfer in the copper-containing nitrite reductases

The reduction of nitrite (NO2-) into nitric oxide (NO), catalyzed by nitrite reductase, is an important reaction in the denitrification pathway. In this study, the catalytic mechanism of the copper-containing nitrite reductase from Alcaligenes xylosoxidans (AxNiR) has been studied using single and multiple turnover experiments at pH 7.0 and is shown to involve two protons. A novel steady-state assay was developed, in which deoxyhemoglobin was employed as an NO scavenger. A moderate solvent kinetic isotope effect (SKIE) of 1.3 +/- 0.1 indicated the involvement of one protonation to the rate-limiting catalytic step. Laser photoexcitation experiments have been used to obtain single turnover data in H2O and D2O, which report on steps kinetically linked to inter-copper electron transfer (ET). In the absence of nitrite, a normal SKIE of approximately 1.33 +/- 0.05 was obtained, suggesting a protonation event that is kinetically linked to ET in substrate-free AxNiR. A nitrite titration gave a normal hyperbolic behavior for the deuterated sample. However, in H2O an unusual decrease in rate was observed at low nitrite concentrations followed by a subsequent acceleration in rate at nitrite concentrations of >10 mM. As a consequence, the observed ET process was faster in D2O than in H2O above 0.1 mM nitrite, resulting in an inverted SKIE, which featured a significant dependence on the substrate concentration with a minimum value of approximately 0.61 +/- 0.02 between 3 and 10 mM. Our work provides the first experimental demonstration of proton-coupled electron transfer in both the resting and substrate-bound AxNiR, and two protons were found to be involved in turnover.

Cell surface proteins in archaeal and bacterial genomes comprising "LVIVD", "RIVW" and "LGxL" tandem sequence repeats are predicted to fold as beta-propeller

Proteins that share even low sequence homologies are known to adopt similar folds. The beta-propeller structural motif is one such example. Identifying sequences that adopt a beta-propeller fold is useful to annotate protein structure and function. Often, tandem sequence repeats provide the necessary signal for identifying beta-propellers in proteins. In our recent analysis to identify cell surface proteins in archaeal and bacterial genomes, we identified some proteins that contain novel tandem repeats "LVIVD", "RIVW" and "LGxL". In this work, based on protein fold predictions and three-dimensional comparative modeling methods, we predicted that these repeat types fold as beta-propeller. Further, the evolutionary trace analysis of all proteins constituting amino acid sequence repeats in beta-propellers suggest that the novel repeats have diverged from a common ancestor.

Redefining Paracoccus denitrificans and Paracoccus pantotrophus and the case for a reassessment of the strains held by international culture collections

An outline of the current taxonomic diversity of the genus Paracoccus is presented. A definitive summary is given of the valid type strains of Paracoccus denitrificans and Paracoccus pantotrophus and of culture collection strains that can be assigned to these species. The case is established for a critical reassessment of the P. denitrificans strains held by international culture collections, to ensure that they are assigned to the correct species.

Binding of RPE65 Fragments to Lipid Monolayers and Identification of Its Partners by Glutathione S-Transferase Pull-Down Assays

RPE65 is the major component of the retinal pigment epithelium (RPE) microsomal membrane, and it plays a critical role in the binding of retinoids involved in the visual cycle. To understand how RPE65 binds to membranes, we have expressed and purified soluble fragments of human RPE65 fused to glutathione S-transferase (GST). The interaction between two fragments of RPE65 (F1 and F2 which include residues 1-125 and 126-250, respectively) and lipid monolayers has been studied by surface pressure, ellipsometry, and surface rheology measurements. Surface pressure and ellipsometry clearly showed a rapid adsorption of F2 to lipid monolayers whereas the kinetics of binding of F1 was much slower. Furthermore, the data suggest that the F2 fragment inserts into the lipid monolayer. Surface rheology showed a clear increase in monolayer rigidity only in the presence of F2, thereby demonstrating high intermolecular interactions of this fragment. This observation is further supported by the GST pull-down assays which demonstrated that F2 cosediments with full-length RPE65, suggesting that RPE65 has the propensity to form clusters or oligomers. The structure homology modeling of RPE65 based on a related family member, apocarotene 15',15'-oxygenase, further suggests that a hydrophobic patch located in the F2 region might be responsible for membrane binding. The present work shows that F2 interacts much stronger with lipid monolayers than does F1, which suggests that the region of RPE65 located between residues 126-250 should be very important for its membrane binding. Moreover, given that these fragments are not acylated, these data also suggest that an effective binding of RPE65 to membranes can be achieved without palmitoylation. Furthermore, GST pull-down assays also indicated that F2 interacts with 11-cis-retinol dehydrogenase, which supports previous data suggesting that it could act as a partner of RPE65.

Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus

The endophytic Gram-negative bacterium Gluconacetobacter diazotrophicus SRT4 secretes a constitutively expressed levansucrase (LsdA, EC 2.4.1.10), which converts sucrose into fructooligosaccharides and levan. The enzyme is included in GH (glycoside hydrolase) family 68 of the sequence-based classification of glycosidases. The three-dimensional structure of LsdA has been determined by X-ray crystallography at a resolution of 2.5 A (1 A=0.1 nm). The structure was solved by molecular replacement using the homologous Bacillus subtilis (Bs) levansucrase (Protein Data Bank accession code 1OYG) as a search model. LsdA displays a five-bladed beta-propeller architecture, where the catalytic residues that are responsible for sucrose hydrolysis are perfectly superimposable with the equivalent residues of the Bs homologue. The comparison of both structures, the mutagenesis data and the analysis of GH68 family multiple sequences alignment show a strong conservation of the sucrose hydrolytic machinery among levansucrases and also a structural equivalence of the Bs levansucrase Ca2+-binding site to the LsdA Cys339-Cys395 disulphide bridge, suggesting similar fold-stabilizing roles. Despite the strong conservation of the sucrose-recognition site observed in LsdA, Bs levansucrase and GH32 family Thermotoga maritima invertase, structural differences appear around residues involved in the transfructosylation reaction.

Structural basis for thermostability of endo-1,5-alpha-L-arabinanase from Bacillus thermodenitrificans TS-3

The crystal structure of a thermostable endo-1,5-alpha-L-arabinanase, ABN-TS, from Bacillus thermodenitrificans TS-3 was determined at 1.9 A to an R-factor of 18.3% and an R-free-factor of 22.5%. The enzyme molecule has a five-bladed beta-propeller fold. The substrate-binding cleft formed across one face of the propeller is open on both sides to allow random binding of several sugar units in the polymeric substrate arabinan. The beta-propeller fold is stabilized through a ring closure. ABN-TS exhibits a new closure-mode involving residues in the N-terminal region: Phe7 to Gly21 exhibit hydrogen bonds and hydrophobic interactions with the first and last blades, and Phe4 links the second and third blades through a hydrogen bond and an aromatic stacking interaction, respectively. The role of the N-terminal region in the thermostability was confirmed with a mutant lacking 16 amino acid residues from the N-terminus of ABN-TS.

The automatic detection of known beta-propeller structural motifs from protein tertiary structure

Following our previous work on the analysis of 'structural plasticity' associated with the beta-propeller structural motifs, we have now developed a simple method that can automatically detect all the known beta-propellers in protein tertiary structure, given a list of Protein Data Bank (PDB) codes as input to the computer program. Our beta-propeller detection (BPD) method identifies the location of beta-propellers in the protein structure, specifies the beta-propeller type, the beta-sheet associated beta-strand pattern and the structurally similar beta-propellers observed in other proteins. When tested on 21,566 proteins in the PDB, the BPD method was capable of correctly identifying all the known 245 beta-propellers described in the structural classification of proteins (SCOP) with the number of false positives detected being less than 0.2%. Forty-one false positives were detected that correspond to eight known protein families. When compared with some of the popular web-based programs that can automatically detect 'structural similarities' between the query and target proteins, our method has the advantage of also being capable of detecting beta-propellers associated with 'structural plasticity' and in situations where the target and query proteins differ in amino acid sequence length.

Y25S Variant of Paracoccus pantotrophus Cytochrome cd1 Provides Insight into Anion Binding by d1 Heme and a Rare Example of a Critical Difference between Solution and Crystal Structures

Tyr25 is a ligand to the active site d1 heme in as isolated, oxidized cytochrome cd1 nitrite reductase from Paracoccus pantotrophus. This form of the enzyme requires reductive activation, a process that involves not only displacement of Tyr25 from the d1 heme but also switching of the ligands at the c heme from bis-histidinyl to His/Met. A Y25S variant retains this bis-histidinyl coordination in the crystal of the oxidized state that has sulfate bound to the d1 heme iron. This Y25S form of the enzyme does not require reductive activation, an observation previously interpreted as meaning that the presence of the phenolate oxygen of Tyr25 is the critical determinant of the requirement for activation. This interpretation now needs re-evaluation because, unexpectedly, the oxidized as prepared Y25S protein, unlike the wild type, has different heme iron ligands in solution at room temperature, as judged by magnetic circular dichroism and electron spin resonance spectroscopies, than in the crystal. In addition, the binding of nitrite and cyanide to oxidized Y25S cytochrome cd1 is markedly different from the wild type enzyme, thus providing insight into the affinity of the oxidized d1 heme ring for anions in the absence of the steric barrier presented by Tyr25.

Magnetic Resonance and Structural Investigations of (Monooxooctaethylchlorinato)iron(III) Chloride and Its Bis(imidazole) Complex

(Monooxooctaethylchlorinato)iron(III) chloride, (oxo-OEC)FeCl, 1, has been investigated by X-ray crystallography and by 1H NMR spectroscopy. Its bis(imidazole-d4) complex has been studied by multidimensional 1H NMR and EPR spectroscopies, and the results are compared to those for the bis(Im-d4) complex of (octaethylchlorinato)iron(III) chloride, (OEC)FeCl, 2. EPR and NMR results show that both [(oxo-OEC)Fe(Im-d4)2]Cl and [(OEC)Fe(Im-d4)2]Cl are low-spin Fe(III) complexes with (d(xy))2 (d(xz),d(yz))3 electronic ground states, both at 4.2 K (EPR spectra) and at ambient temperatures utilized for solution NMR studies. The pattern of chemical shifts of the pyrrole-CH2 and meso protons are similar, with the 8,17-carbons having the largest and the 12,13-carbons having the smallest spin densities in each case, except that [(OEC)Fe(Im-d4)2]Cl has a slightly wider range of pyrrole-CH2 chemical shifts and more resonances are observed for [(oxo-OEC)Fe(Im-d4)2]Cl due to its lower symmetry. Full proton resonance assignments for both complexes have been made from COSY, NOESY, and NOE difference experiments.

Structural plasticity associated with the beta-propeller architecture

The beta-propeller architecture observed in protein tertiary structure and classified into the five different types according to number of 'blades' (or beta-sheets) and a sixth type classified according to the secondary structure composition of the blades (the beta beta alpha beta-molecular unit) is characterized by variations (or plasticity) in the structure. These correspond to the number of beta-strands associated with the blade, the number of amino acid residues associated with equivalent beta-strands in the different blades and the presence of alpha-helices and twisted beta-strands. We have generated a beta-sheet associated beta-strand pattern that may be important for protein structure prediction and modeling. Analysis of the beta-propellers extracted primarily from the SCOP database revealed there are 179 beta-propellers. The examination of the secondary structure corresponding to the beta-propeller using PDBsum that was useful to define the beta-sheet associated beta-strand pattern, combined with visualization on graphics display revealed structural plasticity associated with the beta-propeller architecture. Particularly, the type 6- and 7-bladed beta-propellers known to be associated with sequence and functional diversity are more common and associated with relatively more structural variations compared to the other beta-propeller types.

Speriolin Is a Novel Spermatogenic Cell-specific Centrosomal Protein Associated with the Seventh WD Motif of Cdc20

The fundamental mechanisms of mitosis are conserved throughout evolution in eukaryotes, including ubiquitin-mediated proteolysis of cell cycle regulators by the anaphase-promoting complex/cyclosome. The spindle checkpoint protein Cdc20 activates the anaphase-promoting complex/cyclosome in a substrate-specific manner. It is present in the cytoplasm and concentrated in the centrosomes throughout the cell cycle, accumulates at the kinetochores in metaphase, and is no longer detected following anaphase. However, it is unknown whether Cdc20 has the same activities and distribution during meiosis in male germ cells. We found that in mice, Cdc20 accumulates in the cytoplasm of pachytene spermatocytes during meiosis I, is distributed throughout spermatocytes undergoing meiotic division, and is present in the cytoplasm of postmeiotic spermatids. Several proteins bind to and regulate the function of Cdc20 during mitosis. We identified speriolin and determined that it is a novel spermatogenic cell-specific Cdc20-binding protein, is present in the cytoplasm, and is concentrated at the centrosomes of spermatocytes and spermatids and that a leucine zipper domain is required to target speriolin to the centrosome. The seven tandem WD motifs of Cdc20 probably fold into a seven-blade beta-propeller structure, and we determined that they are required for speriolin binding and for localization of Cdc20 to the centrosomes and nucleus, suggesting that speriolin might regulate or stabilize the folding of Cdc20 during meiosis in spermatogenic cells.

Direct Immobilization of Native Yeast Iso-1 Cytochrome c on Bare Gold: Fast Electron Relay to Redox Enzymes and Zeptomole Protein-Film Voltammetry

Cyclic voltammetry shows that yeast iso-1-cytochrome c (YCC), chemisorbed on a bare gold electrode via Cys102, exhibits fast, reversible interfacial electron transfer (k(0) = 1.8 x 10(3) s(-1)) and retains its native functionality. Vectorially immobilized YCC relays electrons to yeast cytochrome c peroxidase, and to both cytochrome cd(1) nitrite reductase (NIR) and nitric oxide reductase from Paracoccus denitrificans, thereby revealing the mechanistic properties of these enzymes. On a microelectrode, we measured nitrite turnover by approximately 80 zmol (49 000 molecules) of NIR, coadsorbed on 0.65 amol (390 000 molecules) of YCC.

Concerted Structural Changes in the Peptidase and the Propeller Domains of Prolyl Oligopeptidase are Required for Substrate Binding

Prolyl oligopeptidase contains a peptidase domain and its catalytic triad is covered by the central tunnel of a seven-bladed beta-propeller. This domain makes the enzyme an oligopeptidase by excluding large structured peptides from the active site. The apparently rigid crystal structure does not explain how the substrate can approach the catalytic groups. Two possibilities of substrate access were investigated: either blades 1 and 7 of the propeller domain move apart, or the peptidase and/or propeller domains move to create an entry site at the domain interface. Engineering disulfide bridges to the expected oscillating structures prevented such movements, which destroyed the catalytic activity and precluded substrate binding. This indicated that concerted movements of the propeller and the peptidase domains are essential for the enzyme action.

Parameterization and Classification of the Protein Universe via Geometric Techniques

We present a scheme for the classification of 3487 non-redundant protein structures into 1207 non-hierarchical clusters by using recurring structural patterns of three to six amino acids as keys of classification. This results in several signature patterns, which seem to decide membership of a protein in a functional category. The patterns provide clues to the key residues involved in functional sites as well as in protein-protein interaction. The discovered patterns include a "glutamate double bridge" of superoxide dismutase, the functional interface of the serine protease and inhibitor, interface of homo/hetero dimers, and functional sites of several enzyme families. We use geometric invariants to decide superimposability of structural patterns. This allows the parameterization of patterns and discovery of recurring patterns via clustering. The geometric invariant-based approach eliminates the computationally explosive step of pair-wise comparison of structures. The results provide a vast resource for the biologists for experimental validation of the proposed functional sites, and for the design of synthetic enzymes, inhibitors and drugs.

Thermodynamics of heme binding to the HasA(SM) hemophore: effect of mutations at three key residues for heme uptake

HasA(SM) secreted by the Gram-negative bacterium Serratia marcescens belongs to the hemophore family. Its role is to take up heme from host heme carriers and to shuttle it to specific receptors. Heme is linked to the HasA(SM) protein by an unusual axial ligand pair: His32 and Tyr75. The nucleophilic nature of the tyrosine is enhanced by the hydrogen bonding of the tyrosinate to a neighboring histidine in the binding site: His83. We used isothermal titration microcalorimetry to examine the thermodynamics of heme binding to HasA(SM) and showed that binding is strongly exothermic and enthalpy driven: DeltaH = -105.4 kJ x mol(-1) and TDeltaS = -44.3 kJ x mol(-1). We used displacement experiments to determine the affinity constant of HasA(SM) for heme (K(a) = 5.3 x 10(10) M(-1)). This is the first time that this has been reported for a hemophore. We also analyzed the thermodynamics of the interaction between heme and a panel of single, double, and triple mutants of the two axial ligands His32 and Tyr75 and of His83 to assess the implication of each of these three residues in heme binding. We demonstrated that, in contrast to His32, His83 is essential for the binding of heme to HasA(SM), even though it is not directly coordinated to iron, and that the Tyr75/His83 pair plays a key role in the interaction.

Navigation inside a protease: substrate selection and product exit in the tricorn protease from Thermoplasma acidophilum

The proposed pathway and mechanism of substrate entry and product egress in the hexameric D3 symmetric tricorn protease from Thermoplasma acidophilum were explored by crystallographic studies of ligand complexes and by structure-based mutagenesis. Obstruction of the pore within the 7-bladed beta-propeller (beta7) domain by alkylation or oxidation of an engineered double cysteine mutant strongly decreased enzymatic activities. In line herewith, the crystal structure of the tricorn protease in complex with a trideca-peptide inhibitor modifying the catalytic Ser965 revealed part of the peptide trapped inside the channel of the beta7 domain. The cysteine mutation widening the lumen of the 6-bladed beta-propeller (beta6) domain enhanced catalytic activity, which was restored to normal values after its alkylation. A charge reversal mutant at the putative anchor site of the substrate C terminus, R131E-R132E, drastically reduced the proteolytic activity. The complex crystal structure of a peptide inhibitor with a diketo group at the cleavage site mapped the substrate recognition site and confirmed the role of Arg131-Arg132 as an anchor site. Our results strongly suggest the wider beta7 domain to serve as a selective filter and guide of the substrate to the sequestered active site, while the narrower beta6 domain routes the product to the surface. Moreover, we identified the role of Arg131-Arg132 in anchoring the substrate C terminus.

The structure of Neurospora crassa 3-carboxy-cis,cis-muconate lactonizing enzyme, a beta propeller cycloisomerase

Muconate lactonizing enzymes (MLEs) convert cis,cis-muconates to muconolactones in microbes as part of the beta-ketoadipate pathway; some also dehalogenate muconate derivatives of xenobiotic haloaromatics. There are three different MLE classes unrelated by evolution. We present the X-ray structure of a eukaryotic MLE, Neurospora crassa 3-carboxy-cis,cis-muconate lactonizing enzyme (NcCMLE) at 2.5 A resolution, with a seven-bladed beta propeller fold. It is related neither to bacterial MLEs nor to other beta propeller enzymes, but is structurally similar to the G protein beta subunit. It reveals a novel metal-independent cycloisomerase motif unlike the bacterial metal cofactor MLEs. Together, the bacterial MLEs and NcCMLE structures comprise a striking structural example of functional convergence in enzymes for 1,2-addition-elimination of carboxylic acids. NcCMLE and bacterial MLEs may enhance the reaction rate differently: the former by electrophilic catalysis and the latter by electrostatic stabilization of the enolate.

Cryocrystallography of metalloprotein reaction intermediates

Freeze-trapping reaction intermediates in macromolecular crystals is now a proven technique for obtaining their high-resolution structures by X-ray crystallography. The structural study of metalloprotein mechanisms has spearheaded this work, mainly because of the increased availability of single-crystal UV/visible spectrophotometry that enables reaction monitoring in the crystalline state. In particular, through formation of the frozen glass state, the stabilization of intermediates involving dissolved gases has yielded some of the most spectacular results. Metalloprotein systems still dominate this field, and the most recent successes, along with the accompanying advances in methodology, are presented.

Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils

The genetic heterogeneity of nitrite reductase gene (nirK and nirS) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods. nirK gene fragments could be amplified from both soils, whereas nirS gene fragments could be amplified only from the marsh soil. PCR products were cloned and screened by restriction fragment length polymorphism (RFLP), and representative fragments were sequenced. The diversity of nirK clones was lower than the diversity of nirS clones. Among the 54 distinct nirK RFLP patterns identified in the two soils, only one pattern was found in both soils and in each soil two dominant groups comprised >35% of all clones. No dominance and few redundant patterns were seen among the nirS clones. Phylogenetic analysis of deduced amino acids grouped the nirK sequences into five major clusters, with one cluster encompassing most marsh clones and all upland clones. Only a few of the nirK clone sequences branched with those of known denitrifying bacteria. The nirS clones formed two major clusters with several subclusters, but all nirS clones showed less than 80% identity to nirS sequences from known denitrifying bacteria. Overall, the data indicated that the denitrifying communities in the two soils have many members and that the soils have a high richness of different nir genes, especially of the nirS gene, most of which have not yet been found in cultivated denitrifiers.

Novel sequences propel familiar folds

Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.