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Acta Cryst. (2014). A70, C463
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Bacterial pathogens require iron for proliferation and pathogenesis. Pseudomonas aeruginosa is a prevalent Gram-negative opportunistic human pathogen that takes advantage of immunocompromised hosts, and encodes a number of proteins for uptake and utilization of iron. Here we report the crystal structures of PhuS, previously known as the cytoplasmic heme-trafficking protein from P. aeruginosa, in both the apo- and holo-forms. In comparison to its homologue ChuS from Escherichia coli O157:H7, the heme orientation is rotated 1800 across the α-γ axis, which may account for some of the unique functional properties of PhuS. In contrast to previous findings, heme binding does not result in an overall conformational change of PhuS. We employed spectroscopic analysis and CO measurement by gas chromatography to analyze heme degradation, demonstrating that PhuS is capable of degrading heme using ascorbic acid or cytochrome P450 reductase-NADPH as an electron donor, and produces five times more CO than ChuS. Addition of catalase slows down, but does not stop PhuS-catalyzed heme degradation. Through spectroscopic and mass spectrometry analysis, we identified the enzymatic product of heme degradation to be verdoheme. These data taken together suggest that PhuS is a potent heme-degrading enzyme, in addition to its proposed heme-trafficking function.

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Acta Cryst. (2014). A70, C585
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The type II secretion system (T2SS) is sophisticated multiprotein machinery that enables Gram-negative pathogens to secrete a wide range of exoproteins, named virulence factors, into the extracellular environments. In Pseudomonas aeruginosa, the Xcp T2SS is responsible for secreting many virulence factors that induce severe infections. In T2SS, the recognition and binding of secreted exoproteins are conducted by a structure called the pseudopilius tip, which is formed by four minor pseudopilins, including XcpU, XcpV, XcpW and XcpX. These minor pseudopilins form a quaternary complex, which is also involved in the initiation and regulation of the pseudopilus assembly. Although individual structures of these four pseudopilins have been revealed in different organisms, the substrate recognition and binding mechanisms have not been clearly elucidated due to the lack of systematic studies on the whole structures of several complexes formed by these pseudopilins. As a result, the understanding of the structures of these protein complexes will provide useful information for unveiling the mystery of the recognition and binding mechanisms. The establishment of the substrate binding model requires the preparation of stable complex(es) of substrates and certain minor pseudopilin(s). In this work, we aim to gradually elucidate the secretion mechanisms by assembling each component to build up the whole architecture. The structure of XcpV in complex with XcpW has been determined, and other complexes, especially the XcpU-containing binary and ternary complexes, have been stably established and purified. The identification of these complex structures will significantly promote our understandings of the type II secretion mechanisms.

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Acta Cryst. (2014). A70, C831
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The development of heme oxygenase (HO) inhibitors, especially those that are isozyme-selective, promises powerful pharmacological tools to elucidate the regulatory characteristics of the HO system. HO is known to have cytoprotective properties with a role in several disease states; thus, it is an enticing therapeutic target. Traditionally, given their structural similarity with heme, the metalloporphyrins have been used as competitive HO inhibitors. However, given heme's important role in several other proteins (e.g. cytochromes P450, nitric oxide synthase), nonselectivity is an unfortunate side-effect. Reports that azalanstat and other non-porphyrin molecules inhibited HO led to a multi-faceted effort to develop novel compounds as potent, selective inhibitors of HO. This resulted in the creation of non-competitive HO-selective inhibitors, including a subset with isozyme selectivity for HO-1. Using X-ray crystallography, the structures of several complexes of HO-1 with novel inhibitors have been elucidated, providing insightful information regarding the salient features required for inhibitor binding. This included the structural basis for non-competitive inhibition, flexibility and adaptability of the inhibitor binding pocket, and multiple, potential interaction subsites, all of which can be exploited in future drug-design strategies. The structures revealed a common binding mode, despite different structural fragments, with the flexibility to accommodate bulkier substituents via "induced fit". Compounds bind to the distal side of heme through an azole ``anchor" which coordinates with the heme iron. Expansion of the distal pocket, mainly due to distal helix flexibility, allows accommodation of the compounds, with a distal hydrophobic pocket providing further stabilization yet without displacing heme or the critical Asp140 residue. Rather, binding displaces a catalytically critical water molecule and disrupts an ordered hydrogen-bond network involving Asp140.

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Acta Cryst. (2014). A70, C1281
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Inorganic phosphate is an essential component of many biological molecules and processes including cellular signaling, generation of metabolic energy, DNA and RNA, and membrane phospholipids. Organophosphonates, which contain a highly stable carbon-phosphorus bond, are widely used as herbicidal, chelation, anti-scale, and medicinal agents. PhnY and PhnZ consist of a new oxidative catabolic pathway that is employed by marine bacteria to use 2-aminoethylphosphonic acid as a source of inorganic phosphate. PhnZ is notable for catalyzing the oxidative cleavage of a carbon-phosphorus bond using Fe(II) and dioxygen (see figure), despite belonging to a large family of hydrolytic enzymes, the HD-phosphohydrolase superfamily. We have determined structures of PhnZ in complex with its substrate, (R)-2-amino-1-hydroxyethylphosphonate. The structure reveals PhnZ to have an active site containing two Fe ions bound by 4 histidines and 2 aspartates (see figure) that is strikingly similar to the carbon-carbon bond cleaving enzyme, myo-inositol-oxygenase. Site-directed mutagenesis and kinetic analysis with substrate analogues revealed the roles of key active site residues. A 5th histidine that is conserved in the PhnZ subfamily specifically interacts with the substrate 1-hydroxyl. The structure also revealed that PhnZ possesses a unique induced-fit mechanism whereby an active-site aspartate specifically recognizes the 2-amino group of the substrate and toggles the release of an aromatic residue from the active site, thereby creating space for molecular oxygen bind to the second Fe ion. Structural comparisons of PhnZ reveal an evolutionary connection between Fe(II)-dependent hydrolysis of phosphate esters and oxidative carbon-phosphorus or carbon-carbon bond cleavage, thus uniting the diverse chemistries that are found in the HD superfamily.

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Acta Cryst. (2014). A70, C1408
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The 2-oxoglutarate/Fe(II)-dependent oxygenases (2OG oxygenases) are a large family of proteins that share a similar overall three-dimensional structure and catalyze a diverse array of oxidation reactions. The Jumonji C (JmjC)-domain containing proteins represent an important subclass of the 2OG oxygenase family that typically catalyze protein hydroxylation; however, recently other reactions have been identified, such as tRNA modification. The E. coli gene, ycfD, was predicted to be a JmjC-domain containing protein of unknown function based on primary sequence. Recently YcfD was determined to act as a ribosomal oxygenase, hydroxylating an arginine residue on the 50S ribosomal protein L-16 (RL-16). We have determined the crystal structure of YcfD at 2.7 Å resolution, revealing that YcfD is structurally similar to known JmjC proteins and possesses the characteristic double stranded β-helix fold or cupin domain. Separate from the cupin domain, an additional globular module termed -helical arm mediates dimerization of YcfD. We further have shown that 2-oxoglutarate binds to YcfD using isothermal titration calorimetry and identified R140 and S116 as key 2OG binding residues using mutagenesis which, together with the iron location and structural similarity with other cupin family members, allowed identification of the active site. Structural homology to ribosomal assembly proteins combined with GST-YcfD pull-down of a ribosomal protein and docking of RL-16 to the YcfD active site support the role of YcfD in regulation of bacterial ribosome assembly. Furthermore, overexpression of YcfD is shown to inhibit cell growth signifying a toxic effect on ribosome assembly.

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Acta Cryst. (2014). A70, C1499
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The inner membrane protein E. coli tyrosine kinase (Etk) is part of a large protein complex that assembles and exports capsular polysaccharide (CPS) in Gram-negative bacteria. Etk interacts with an outer membrane protein channel, YccZ (1), and regulates CPS export through autophosphorylation of a tyrosine cluster in its C-terminal tail. Previous work resulted in the structure of the isolated Etk C-terminal kinase domain (2). In the present study, the full-length protein has been purified and characterized in vitro. When purified in n-dodecyl-β-D-maltoside (DDM), Etk full length retains autophosphorylation activity, but is not suitable for crystallization because it severely aggregates and degrades. Using the main degradation product, a truncation containing the N-terminal domain (interacts with YccZ) and both transmembrane helices was designed. Truncated Etk does not further degrade and exists as a mixture of monomers and dimers when solubilized by five detergents as determined by size-exclusion chromatography and analytical ultracentrifugation. Crystals have been successfully grown when the protein is solubilized in DDM or n-decyl-β-D-maltoside (DM). The most promising crystals (DDM, 0.1 M MES pH 6.0, 1-5% PEG 3000, 20-30% PEG 200) have been reproduced and optimized with the assistance of a colorimetric assay (3). This assay relies on a reaction between 2,6-dimethylphenol, sulfuric acid, and the sugar head group of certain detergents to accurately quantify detergent in crystallization samples with minimal sample loss. Additive screening also revealed that MgCl2 improves crystallization. Optimization of this crystallization condition has significantly improved reproducibility of these crystals, but x-ray diffraction is limited to 6.5 Å. Current work is focused on reproducing and optimizing a second crystallization lead (DM, 0.1 M KH2PO4 pH 7.5, 32% PEG 400, 0.1 M KCl).
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