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1.  The Human Mixed Lineage Leukemia 5 (MLL5), a Sequentially and Structurally Divergent SET Domain-Containing Protein with No Intrinsic Catalytic Activity 
PLoS ONE  2016;11(11):e0165139.
Mixed Lineage Leukemia 5 (MLL5) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. Chromatin binding is ensured by its plant homeodomain (PHD) through a direct interaction with the N-terminus of histone H3 (H3). In addition, MLL5 contains a Su(var)3-9, Enhancer of zeste, Trithorax (SET) domain, a protein module that usually displays histone lysine methyltransferase activity. We report here the crystal structure of the unliganded SET domain of human MLL5 at 2.1 Å resolution. Although it shows most of the canonical features of other SET domains, both the lack of key residues and the presence in the SET-I subdomain of an unusually large loop preclude the interaction of MLL5 SET with its cofactor and substrate. Accordingly, we show that MLL5 is devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptides. Hence, the three dimensional structure of MLL5 SET domain unveils the structural basis for its lack of methyltransferase activity and suggests a new regulatory mechanism.
PMCID: PMC5094779  PMID: 27812132
2.  Evidence for a Functional O-Linked N-Acetylglucosamine (O-GlcNAc) System in the Thermophilic Bacterium Thermobaculum terrenum* 
The Journal of Biological Chemistry  2015;290(51):30291-30305.
Background: Protein O-GlcNAcylation is essential for function and stability of many proteins in metazoa and is essential for development.
Results: Thermobaculum terrenum encodes a functional O-GlcNAc hydrolase and a conserved O-GlcNAc-transferase.
Conclusion: T. terrenum is the first known bacterium to possess the components for a functional O-GlcNAc system.
Significance: T. terrenum could become a reductionist model to study protein O-GlcNAcylation on an organism level.
Post-translational modification of proteins is a ubiquitous mechanism of signal transduction in all kingdoms of life. One such modification is addition of O-linked N-acetylglucosamine to serine or threonine residues, known as O-GlcNAcylation. This unusual type of glycosylation is thought to be restricted to nucleocytoplasmic proteins of eukaryotes and is mediated by a pair of O-GlcNAc-transferase and O-GlcNAc hydrolase enzymes operating on a large number of substrate proteins. Protein O-GlcNAcylation is responsive to glucose and flux through the hexosamine biosynthetic pathway. Thus, a close relationship is thought to exist between the level of O-GlcNAc proteins within and the general metabolic state of the cell. Although isolated apparent orthologues of these enzymes are present in bacterial genomes, their biological functions remain largely unexplored. It is possible that understanding the function of these proteins will allow development of reductionist models to uncover the principles of O-GlcNAc signaling. Here, we identify orthologues of both O-GlcNAc cycling enzymes in the genome of the thermophilic eubacterium Thermobaculum terrenum. The O-GlcNAcase and O-GlcNAc-transferase are co-expressed and, like their mammalian orthologues, localize to the cytoplasm. The O-GlcNAcase orthologue possesses activity against O-GlcNAc proteins and model substrates. We describe crystal structures of both enzymes, including an O-GlcNAcase·peptide complex, showing conservation of active sites with the human orthologues. Although in vitro activity of the O-GlcNAc-transferase could not be detected, treatment of T. terrenum with an O-GlcNAc-transferase inhibitor led to inhibition of growth. T. terrenum may be the first example of a bacterium possessing a functional O-GlcNAc system.
PMCID: PMC4683255  PMID: 26491011
electron microscopy (EM); enzyme kinetics; glycosyltransferase; Gram-positive bacteria; O-GlcNAcylation; O-linked N-acetylglucosamine (O-GlcNAc); O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT); protein structure; Thermobaculum terrenum
3.  Virulence Regulation with Venus Flytrap Domains: Structure and Function of the Periplasmic Moiety of the Sensor-Kinase BvgS 
PLoS Pathogens  2015;11(3):e1004700.
Two-component systems (TCS) represent major signal-transduction pathways for adaptation to environmental conditions, and regulate many aspects of bacterial physiology. In the whooping cough agent Bordetella pertussis, the TCS BvgAS controls the virulence regulon, and is therefore critical for pathogenicity. BvgS is a prototypical TCS sensor-kinase with tandem periplasmic Venus flytrap (VFT) domains. VFT are bi-lobed domains that typically close around specific ligands using clamshell motions. We report the X-ray structure of the periplasmic moiety of BvgS, an intricate homodimer with a novel architecture. By combining site-directed mutagenesis, functional analyses and molecular modeling, we show that the conformation of the periplasmic moiety determines the state of BvgS activity. The intertwined structure of the periplasmic portion and the different conformation and dynamics of its mobile, membrane-distal VFT1 domains, and closed, membrane-proximal VFT2 domains, exert a conformational strain onto the transmembrane helices, which sets the cytoplasmic moiety in a kinase-on state by default corresponding to the virulent phase of the bacterium. Signaling the presence of negative signals perceived by the periplasmic domains implies a shift of BvgS to a distinct state of conformation and activity, corresponding to the avirulent phase. The response to negative modulation depends on the integrity of the periplasmic dimer, indicating that the shift to the kinase-off state implies a concerted conformational transition. This work lays the bases to understand virulence regulation in Bordetella. As homologous sensor-kinases control virulence features of diverse bacterial pathogens, the BvgS structure and mechanism may pave the way for new modes of targeted therapeutic interventions.
Author Summary
Bacteria make use of two-component transduction systems, composed of a sensor-kinase and a response regulator, to perceive environmental signals and orchestrate an appropriate response. The virulence regulon of the whooping cough agent Bordetella pertussis is controlled by the two-component system BvgAS. The sensor-kinase BvgS harbor extra-cytoplasmic Venus flytrap perception domains similar to those found in neuronal receptors, and it is the prototype of a large bacterial protein family. We report the atomic structure of the extra-cytoplasmic moiety of BvgS, which shows a novel dimeric arrangement. We show that the virulent phase of B. pertussis that occurs by default corresponds to a specific conformation of BvgS generated by the periplasmic architecture itself and by the differential dynamics of its Venus flytrap domains. The perception of negative signals by the periplasmic domains causes BvgS to shift to a different conformation that corresponds to the avirulent phase of the bacteria. In addition to contributing to our understanding of virulence regulation by B. pertussis at a time of whooping cough re-emergence, this study also paves the way to the mechanistic exploration of the homologous sensor-kinases found in various bacterial pathogens.
PMCID: PMC4352136  PMID: 25738876
4.  Crystal structure of human CRMP-4: correction of intensities for lattice-translocation disorder 
Crystals of human CRMP-4 showed severe lattice-translocation disorder. Intensities were demodulated using the so-called lattice-alignment method and a new more general method with simplified parameterization, and the structure is presented.
Collapsin response mediator proteins (CRMPs) are cytosolic phosphoproteins that are mainly involved in neuronal cell development. In humans, the CRMP family comprises five members. Here, crystal structures of human CRMP-4 in a truncated and a full-length version are presented. The latter was determined from two types of crystals, which were either twinned or partially disordered. The crystal disorder was coupled with translational NCS in ordered domains and manifested itself with a rather sophisticated modulation of intensities. The data were demodulated using either the two-lattice treatment of lattice-translocation effects or a novel method in which demodulation was achieved by independent scaling of several groups of intensities. This iterative protocol does not rely on any particular parameterization of the modulation coefficients, but uses the current refined structure as a reference. The best results in terms of R factors and map correlation coefficients were obtained using this new method. The determined structures of CRMP-4 are similar to those of other CRMPs. Structural comparison allowed the confirmation of known residues, as well as the identification of new residues, that are important for the homo- and hetero-oligomerization of these proteins, which are critical to nerve-cell development. The structures provide further insight into the effects of medically relevant mutations of the DPYSL-3 gene encoding CRMP-4 and the putative enzymatic activities of CRMPs.
PMCID: PMC4051505  PMID: 24914979
CRMP-4; lattice-translocation disorder
5.  JLigand: a graphical tool for the CCP4 template-restraint library 
The CCP4 template-restraint library defines restraints for biopolymers, their modifications and ligands that are used in macromolecular structure refinement. JLigand is a graphical editor for generating descriptions of new ligands and covalent linkages.
Biological macromolecules are polymers and therefore the restraints for macromolecular refinement can be subdivided into two sets: restraints that are applied to atoms that all belong to the same monomer and restraints that are associated with the covalent bonds between monomers. The CCP4 template-restraint library contains three types of data entries defining template restraints: descriptions of monomers and their modifications, both used for intramonomer restraints, and descriptions of links for intermonomer restraints. The library provides generic descriptions of modifications and links for protein, DNA and RNA chains, and for some post-translational modifications including glycosylation. Structure-specific template restraints can be defined in a user’s additional restraint library. Here, JLigand, a new CCP4 graphical interface to LibCheck and REFMAC that has been developed to manage the user’s library and generate new monomer entries is described, as well as new entries for links and associated modifications.
PMCID: PMC3322602  PMID: 22505263
macromolecular refinement; restraint library; molecular graphics
6.  Crystal structure of the FimD usher bound to its cognate FimC:FimH substrate 
Nature  2011;474(7349):49-53.
Type 1 pili are the archetypal representative of a widespread class of adhesive multisubunit fibres in Gram-negative bacteria. During pilus assembly, subunits dock as chaperone-bound complexes to an usher, which catalyzes their polymerization and mediates pilus translocation across the outer membrane. We report the crystal structure of the full-length FimD usher bound to the FimC:FimH chaperone:adhesin complex and that of the unbound form of the FimD translocation domain. The FimD:FimC:FimH structure shows FimH inserted inside the FimD 24-stranded β-barrel translocation channel. FimC:FimH is held in place through interactions with the two C-terminal periplasmic domains of FimD, a binding mode confirmed in solution by electron paramagnetic resonance spectroscopy. To accommodate FimH, the usher plug domain is displaced from the barrel lumen to the periplasm, concomitant with a dramatic conformational change in the β-barrel. The N-terminal domain of FimD is observed in an ideal position to catalyse incorporation of a newly recruited chaperone:subunit complex. The FimD:FimC:FimH structure provides unique insights into the pilus subunit incorporation cycle, and captures the first view of a protein transporter in the act of secreting its cognate substrate.
PMCID: PMC3162478  PMID: 21637253
7.  Structural rearrangement accompanying ligand binding in the GAF domain of CodY from Bacillus subtilis 
Journal of molecular biology  2009;390(5):1007-1018.
The GAF domain is a simple module widespread in proteins of diverse function including cell signalling proteins and transcription factors. Its structure, typically spanning 150 residues, has three tiers; a basal layer of two or more α-helices, a middle layer of β-pleated sheet and a top layer formed by segments of the polypeptide that connect strands of the β-sheet. In structures of GAF domains in complex with their effectors, these polypeptide segments envelop the ligand enclosing it in a cavity whose base is formed by the β-sheet, so that ligand binding and release must be accompanied by conformational rearrangements of the distal portion of the structure. Descriptions of binding are presently limited by the absence of a GAF domain for which both liganded and unliganded structures are known. Earlier, we solved the crystal structure of the GAF domain of CodY, a branched chain amino acid and GTP responsive regulator of the transcription of stationary phase and virulence genes in Bacillus, in complexes with isoleucine and valine. Here, we report the structure of this domain in its unliganded form, allowing definition of the structural changes accompanying ligand binding. The core of the protein and its dimerisation interface are essentially unchanged in agreement with circular dichroism spectroscopy experiments that show that the secondary structure composition is unperturbed by ligand binding. There is however, extensive refolding of the binding site loops, with up to 15 Å movements of the coiled segment linking β3 and β4, such that in the absence of the ligand, the binding pocket is not formed. The implications of these structural rearrangements for ligand affinity and specificity are discussed. Finally, saturation transfer difference NMR spectroscopy showed binding of isoleucine, but not GTP, to the GAF domain suggesting that the two cofactors do not have a common binding site.
PMCID: PMC3128921  PMID: 19500589
GAF domain; conformational change; transcription regulation; Bacillus subtilis; branched chain amino acids
8.  REFMAC5 for the refinement of macromolecular crystal structures 
The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described.
This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.
PMCID: PMC3069751  PMID: 21460454
REFMAC5; refinement
9.  The Structure and Interactions of SpoIISA and SpoIISB, a Toxin-Antitoxin System in Bacillus subtilis* 
The Journal of Biological Chemistry  2010;286(8):6808-6819.
Spore formation in Bacillus subtilis begins with an asymmetric cell division, following which differential gene expression is established by alternative compartment-specific RNA polymerase σ factors. The spoIISAB operon of B. subtilis was identified as a locus whose mutation leads to increased activity of the first sporulation-specific sigma factor, σF. Inappropriate spoIISA expression causes lysis of vegetatively growing B. subtilis cells and Escherichia coli cells when expressed heterologously, effects that are countered by co-expression of spoIISB, identifying SpoIISA-SpoIISB as a toxin-antitoxin system. SpoIISA has three putative membrane-spanning segments and a cytoplasmic domain. Here, the crystal structure of a cytoplasmic fragment of SpoIISA (CSpoIISA) in complex with SpoIISB has been determined by selenomethionine-multiwavelength anomalous dispersion phasing to 2.5 Å spacing, revealing a CSpoIISA2·SpoIISB2 heterotetramer. CSpoIISA has a single domain α/β structure resembling a GAF domain with an extended α-helix at its N terminus. The two CSpoIISA protomers form extensive interactions through an intermolecular four-helix bundle. Each SpoIISB chain is highly extended and lacking tertiary structure. The SpoIISB chains wrap around the CSpoIISA dimer, forming extensive interactions with both CSpoIISA protomers. CD spectroscopy experiments indicate that SpoIISB is a natively disordered protein that adopts structure only in the presence of CSpoIISA, whereas surface plasmon resonance experiments revealed that the CSpoIISA·SpoIISB complex is stable with a dissociation constant in the nanomolar range. The results are interpreted in relation to sequence conservation and mutational data, and possible mechanisms of cell killing by SpoIISA are discussed.
PMCID: PMC3057836  PMID: 21147767
Bacterial Toxins; Crystal Structure; Membrane Proteins; Protein Structure; Protein-Protein Interactions; Native Disorder; Sporulation; Toxin-Antitoxin
10.  Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein 
Defects in the human Shwachman-Bodian-Diamond syndrome (SBDS) protein-coding gene lead to the autosomal recessive disorder characterised by bone marrow dysfunction, exocrine pancreatic insufficiency and skeletal abnormalities. This protein is highly conserved in eukaryotes and archaea but is not found in bacteria. Although genomic and biophysical studies have suggested involvement of this protein in RNA metabolism and in ribosome biogenesis, its interacting partners remain largely unknown.
We determined the crystal structure of the SBDS orthologue from Methanothermobacter thermautotrophicus (mthSBDS). This structure shows that SBDS proteins are highly flexible, with the N-terminal FYSH domain and the C-terminal ferredoxin-like domain capable of undergoing substantial rotational adjustments with respect to the central domain. Affinity chromatography identified several proteins from the large ribosomal subunit as possible interacting partners of mthSBDS. Moreover, SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments, combined with electrophoretic mobility shift assays (EMSA) suggest that mthSBDS does not interact with RNA molecules in a sequence specific manner.
It is suggested that functional interactions of SBDS proteins with their partners could be facilitated by rotational adjustments of the N-terminal and the C-terminal domains with respect to the central domain. Examination of the SBDS protein structure and domain movements together with its possible interaction with large ribosomal subunit proteins suggest that these proteins could participate in ribosome function.
PMCID: PMC2695463  PMID: 19454024
11.  Model preparation in MOLREP and examples of model improvement using X-ray data 
The default model-preparation scheme of MOLREP is described. Two examples are presented of model improvement using X-ray data.
The success of molecular replacement is critically dependent on the quality of the search model. Several model-preparation procedures are integrated in the molecular-replacement program MOLREP. These include model modification on the basis of amino-acid sequence alignment and model correction based on analysis of the solvent-accessibility of the atoms. The packing function used in MOLREP for the translational search is explained in the context of model preparation. In difficult cases, bioinformatics-based modifications are not sufficient for successful molecular replacement. An approach implemented in MOLREP for solving cases with translational noncrystallographic symmetry is an example of model preparation in which analysis of X-ray data plays an essential role. In addition, two examples are presented in which the X-ray data were used to refine partial models for subsequent use in molecular replacement.
PMCID: PMC2394799  PMID: 18094465
MOLREP; model preparation; molecular replacement
12.  Surprises and pitfalls arising from (pseudo)symmetry 
The presence of pseudosymmetry can cause problems in structure determination and refinement. The relevant background and representative examples are presented.
It is not uncommon for protein crystals to crystallize with more than a single molecule per asymmetric unit. When more than a single molecule is present in the asymmetric unit, various pathological situations such as twinning, modulated crystals and pseudo translational or rotational symmetry can arise. The presence of pseudosymmetry can lead to uncertainties about the correct space group, especially in the presence of twinning. The background to certain common pathologies is presented and a new notation for space groups in unusual settings is introduced. The main concepts are illustrated with several examples from the literature and the Protein Data Bank.
PMCID: PMC2394827  PMID: 18094473
pathology; twinning; pseudosymmetry
13.  NCS-constrained exhaustive search using oligomeric models 
Three difficult MR cases are reported in which the orientation of a search oligomer or its internal parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches. Such an exhaustive search was feasible because of constraints on the model parameters derived from the self-rotation function.
The efficiency of the cross-rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.
PMCID: PMC2394828  PMID: 18094472
molecular replacement; exhaustive search
14.  Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors 
Nucleic Acids Research  2007;35(19):6451-6457.
Concerted, stochastic and sequential mechanisms of action have been proposed for different hexameric AAA+ molecular motors. Here we report the crystal structure of the E1 helicase from bovine papillomavirus, where asymmetric assembly is for the first time observed in the absence of nucleotide cofactors and DNA. Surprisingly, the ATP-binding sites adopt specific conformations linked to positional changes in the DNA-binding hairpins, which follow a wave-like trajectory, as observed previously in the E1/DNA/ADP complex. The protein's assembly thus maintains such an asymmetric state in the absence of DNA and nucleotide cofactors, allowing consideration of the E1 helicase action as the propagation of a conformational wave around the protein ring. The data imply that the wave's propagation within the AAA+ domains is not necessarily coupled with a strictly sequential hydrolysis of ATP. Since a single ATP hydrolysis event would affect the whole hexamer, such events may simply serve to rectify the direction of the wave's motion.
PMCID: PMC2095799  PMID: 17881379
15.  Crystal structure of Bacillus cereus HlyIIR, a transcriptional regulator of the gene for pore-forming toxin Hemolysin II 
Journal of molecular biology  2006;365(3):825-834.
Production of Bacillus cereus and Bacillus anthracis toxins is controlled by a number of transcriptional regulators. Here we report the crystal structure of Bacillus cereus HlyIIR, a regulator of the gene encoding the pore-forming toxin hemolysin II. We show that HlyIIR forms a tight dimer with a fold and overall architecture similar to the TetR family of repressors. A remarkable feature of the structure is a large internal cavity with a volume of 550 Å3 suggesting that the activity of HlyIIR is modulated by binding of a ligand, which triggers the toxin production. Virtual ligand library screening shows that this pocket can accommodate compounds with molecular masses of up to 400-500 Da. Based on structural data and previous biochemical evidence, we propose a model for HlyIIR interaction with the DNA.
PMCID: PMC1828608  PMID: 17097673
HlyIIR; X-ray crystallography; DNA-binding; TetR family; Hemolysin II
16.  Crystal Structure of Bacillus cereus HlyIIR, a Transcriptional Regulator of the Gene for Pore-forming Toxin Hemolysin II 
Journal of Molecular Biology  2007;365(3):825-834.
Production of Bacillus cereus and Bacillus anthracis toxins is controlled by a number of transcriptional regulators. Here we report the crystal structure of B. cereus HlyIIR, a regulator of the gene encoding the pore-forming toxin hemolysin II. We show that HlyIIR forms a tight dimer with a fold and overall architecture similar to the TetR family of repressors. A remarkable feature of the structure is a large internal cavity with a volume of 550 Å3 suggesting that the activity of HlyIIR is modulated by binding of a ligand, which triggers the toxin production. Virtual ligand library screening shows that this pocket can accommodate compounds with molecular masses of up to 400–500 Da. Based on structural data and previous biochemical evidence, we propose a model for HlyIIR interaction with the DNA.
PMCID: PMC1828608  PMID: 17097673
HlyII, hemolysin II; RNAP, RNA-polymerase; SELEX, systematic evolution of ligands by exponential enrichment; SeMet, selenomethionine; HlyIIR; X-ray crystallography; DNA-binding; TetR family; hemolysin II

Results 1-16 (16)