Prominent Groove Research Articles

Crystal structures of the GH18 domain of the bifunctional peroxiredoxin-chitinase CotE from Clostridium difficile.

CotE is a coat protein that is present in the spores of Clostridium difficile, an obligate anaerobic bacterium and a pathogen that is a leading cause of antibiotic-associated diarrhoea in hospital patients. Spores serve as the agents of disease transmission, and CotE has been implicated in their attachment to the gut epithelium and subsequent colonization of the host. CotE consists of an N-terminal peroxiredoxin domain and a C-terminal chitinase domain. Here, a C-terminal fragment of CotE comprising residues 349-712 has been crystallized and its structure has been determined to reveal a core eight-stranded β-barrel fold with a neighbouring subdomain containing a five-stranded β-sheet. A prominent groove running across the top of the barrel is lined by residues that are conserved in family 18 glycosyl hydrolases and which participate in catalysis. Electron density identified in the groove defines the pentapeptide Gly-Pro-Ala-Met-Lys derived from the N-terminus of the protein following proteolytic cleavage to remove an affinity-purification tag. These observations suggest the possibility of designing peptidomimetics to block C. difficile transmission.

Identification of the active site of human mitochondrial malonyl-coenzyme a decarboxylase: A combined computational study.

Malonyl-CoA decarboxylase (MCD) can control the level of malonyl-CoA in cell through the decarboxylation of malonyl-CoA to acetyl-CoA, and plays an essential role in regulating fatty acid metabolism, thus it is a potential target for drug discovery. However, the interactions of MCD with CoA derivatives are not well understood owing to unavailable crystal structure with a complete occupancy in the active site. To identify the active site of MCD, molecular docking and molecular dynamics simulations were performed to explore the interactions of human mitochondrial MCD (HmMCD) and CoA derivatives. The findings reveal that the active site of HmMCD indeed resides in the prominent groove which resembles that of CurA. However, the binding modes are slightly different from the one observed in CurA due to the occupancy of the side chain of Lys183 from the N-terminal helical domain instead of the adenine ring of CoA. The residues 300 - 305 play an essential role in maintaining the stability of complex mainly through hydrogen bond interactions with the pyrophosphate moiety of acetyl-CoA. Principle component analysis elucidates the conformational distribution and dominant concerted motions of HmMCD. MM_PBSA calculations present the crucial residues and the major driving force responsible for the binding of acetyl-CoA. These results provide useful information for understanding the interactions of HmMCD with CoA derivatives. Proteins 2016; 84:792-802. © 2016 Wiley Periodicals, Inc.

Structural Studies Reveal the Functional Modularity of the Scc2-Scc4 Cohesin Loader.

The remarkable accuracy of eukaryotic cell division is partly maintained by the cohesin complex acting as a molecular glue to prevent premature sister chromatid separation. The loading of cohesin onto chromosomes is catalyzed by the Scc2-Scc4 loader complex. Here, we report the crystal structure of Scc4 bound to the N terminus of Scc2 and show that Scc4 is a tetratricopeptide repeat (TPR) superhelix. The Scc2 N terminus adopts an extended conformation and is entrapped by the core of the Scc4 superhelix. Electron microscopy (EM) analysis reveals that the Scc2-Scc4 loader complex comprises three domains: a head, body, and hook. Deletion studies unambiguously assign the Scc2N-Scc4 as the globular head domain, whereas in vitro cohesin loading assays show that the central body and the hook domains are sufficient to catalyze cohesin loading onto circular DNA, but not chromatinized DNA in vivo, suggesting a possible role for Scc4 as a chromatin adaptor.

Crystal structure of the pilotin from the enterohemorrhagic Escherichia coli type II secretion system

Bacteria contain several sophisticated macromolecular machineries responsible for translocating proteins across the cell envelope. One prominent example is the type II secretion system (T2SS), which contains a large outer membrane channel, called the secretin. These gated channels require specialized proteins, so-called pilotins, to reach and assemble in the outer membrane. Here we report the crystal structure of the pilotin GspS from the T2SS of enterohemorrhagic Escherichia coli (EHEC), an important pathogen that can cause severe disease in cases of food poisoning. In this four-helix protein, the straight helix α2, the curved helix α3 and the bent helix α4 surround the central N-terminal helix α1. The helices of GspS create a prominent groove, mainly formed by side chains of helices α1, α2 and α3. In the EHEC GspS structure this groove is occupied by extra electron density which is reminiscent of an α-helix and corresponds well with a binding site observed in a homologous pilotin. The residues forming the groove are well conserved among homologs, pointing to a key role of this groove in this class of T2SS pilotins. At the same time, T2SS pilotins in different species can be entirely different in structure, and the pilotins for secretins in non-T2SS machineries have yet again unrelated folds, despite a common function. It is striking that a common complex function, such as targeting and assembling an outer membrane multimeric channel, can be performed by proteins with entirely different folds.

Morphological Characteristics of the Vallate Papillae of the One‐Humped Camel (Camelus dromedarius)

In this study, the morphology of the vallate papillae of camel was investigated using gross, light and scanning electron microscopy as well as immunohistochemistry. Vallate papillae were arranged along an identical line on each side of the lingual torus and revealed remarkable individual differences. However, each papilla - round or flat, small or large, single or paired - was surrounded by a prominent groove and an annular pad. Based on our findings, postnatal development and formation of new papillae occur in camel. Microscopically, taste buds were constantly observed along the medial wall epithelium, and in the papillary wall epithelium on both sides of the secondary groove apparently separating the vallate papillae. In addition, an aggregation of taste buds was occasionally observed at the bottom of the lateral wall epithelium. Using SEM, we observed several pits and microplicae on the surface of papillae as well as distinct taste pores on the peripheral parts of the dorsal surface. We demonstrated immunoreactivity of α-gustducin only in mature taste buds. We conclude that the morphological features and microstructure of vallate papillae are a characteristic feature in camel compared to other ruminants. These features might have evolved to assist the camel in the manipulation and tasting of thin organic stiff plants that grow in its environment and therefore might have related to the feeding habits of the animal.

An Unusual Pulmonary Mass With Mediastinal Invasion and Multiple Intrapulmonary Nodules in a 52-Year-Old Man

An Unusual Pulmonary Mass With Mediastinal Invasion and Multiple Intrapulmonary Nodules in a 52-Year-Old Man

Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding

Starch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase.

Crystal structure of human retinoblastoma binding protein 9

Crystal structure of human retinoblastoma binding protein 9

Structure of the Oligosaccharyl Transferase Complex at 12 Å Resolution

Oligosaccharyl transferase (OT) catalyzes the transfer of a lipid-linked oligosaccharide to the nascent polypeptide emerging from the translocon. Currently, there is no structural information on the membrane-embedded OT complex, which consists of eight different polypeptide chains. We report a 12 A resolution cryo-electron microscopy structure of OT from yeast. We mapped the locations of four essential OT subunits through a maltose-binding protein fusion strategy. OT was found to have a large domain in the lumenal side of endoplasmic reticulum where the catalysis occurs. The lumenal domain mainly comprises the catalytic Stt3p, the donor substrate-recognizing Wbp1p, and the acceptor substrate-recognizing Ost1p. A prominent groove was observed between these subunits, and we propose that the nascent polypeptide from the translocon threads through this groove while being scanned by the Ost1p subunit for the presence of the glycosylation sequon.

Functional Reconstruction of the Philtral Ridge and Dimple in the Repaired Cleft Lip

Our report describes a simple method of functional reconstruction of the philtral ridge in patients with repaired cleft lip. Philtral reconstruction was performed in 21 children with dehiscence of the orbicularis oris in repaired cleft lip. Prominent groove at the philtral column and lateral bulging during maximal "pucker" were the indications. First, the abnormally inserted orbicularis muscle is freed and realigned in a normal horizontal orientation. The muscle is vertically incised and repaired with vertical mattress sutures, spreading out the muscle to increase the thickness of the philtral ridge. The philtral ridge is accentuated by deepening the dimple with a dermal suture at the midline. Postoperative evaluation was performed at 8-18 months (mean; 13.1 months). The philtrum was evaluated by a panel using two visual scales. Eminence of the philtral ridge was scored by a five-point grading scale and the philtral dimple was scored by a three-point grading scale, both at resting and at maximal pucker. Preoperative scores showed the philtral ridge to be from "prominent groove" to "flat" at maximal pucker and at rest, respectively. Postoperative scores showed improvement of the philtral ridge to "less prominent than the normal philtral ridge" both at rest and at maximal pucker. The philtral dimple preoperative scores ranged from "no dimple" to "slight dimple" and postoperative improvement to "slight dimple" to "prominent dimple." This technique of functional reconstruction of the philtrum gave satisfactory results in formation of the philtral ridge and dimple, both at rest and at maximal pucker.

A Novel Dimer Interface and Conformational Changes Revealed by an X-ray Structure of B. subtilis SecA

The SecA ATPase moves polypeptides post-translationally across the plasma membrane of eubacteria, but the mechanism of transport is still unclear. We describe the crystal structure of a novel dimeric form of Bacillus subtilis SecA. Dimerization of SecA occurs at the prominent groove formed by the nucleotide binding domain 2 (nbd2) and the preprotein cross-linking (ppx) domain. The dimer interface is very large, burying approximately 5400 Å 2 of solvent accessible surface per monomer. Single cysteine disulfide cross-linking shows the presence of this novel SecA dimer in solution. In addition, other dimers also exist in solution, arguing that they all are in equilibrium with monomeric SecA and supporting the idea that the monomer may be the functional species. Dimerization of SecA causes an α-helix of one subunit to convert to a short β-strand that participates in β-sheet formation with strands in the other subunit. This conversion of secondary structure elements occurs close to the connection between the nbd1 and ppx domains, a potential site of interaction with translocation substrate. Comparing the different X-ray structures of B. subtilis SecA suggests that small changes in the nucleotide binding domains could be amplified via helix 1 of the helical scaffold domain (hsd) to generate larger movements of the domains involved in polypeptide binding.

Structure of Human FIH-1 Reveals a Unique Active Site Pocket and Interaction Sites for HIF-1 and von Hippel-Lindau

The master switch of cellular hypoxia responses, hypoxia-inducible factor 1 (HIF-1), is hydroxylated by factor inhibiting HIF-1 (FIH-1) at a conserved asparagine residue under normoxia, which suppresses transcriptional activity of HIF-1 by abrogating its interaction with transcription coactivators. Here we report the crystal structure of human FIH-1 at 2.8-A resolution. The structural core of FIH-1 consists of a jellyroll-like beta-barrel containing the conserved ferrous-binding triad residues, confirming that FIH-1 is a member of the 2-oxoglutarate-dependent dioxygenase family. Except for the core structure and triad residues, FIH-1 has many structural deviations from other family members including N- and C-terminal insertions and various deletions in the middle of the structure. The ferrous-binding triad region is highly exposed to the solvent, which is connected to a prominent groove that may bind to a helix near the hydroxylation site of HIF-1. The structure, which is in a dimeric state, also reveals the putative von Hippel-Lindau-binding site that is distinctive to the putative HIF-1-binding site, supporting the formation of the ternary complex by FIH-1, HIF-1, and von Hippel-Lindau. The unique environment of the active site and cofactor-binding region revealed in the structure should allow design of selective drugs that can be used in ischemic diseases to promote hypoxia responses.

Crystal structure of the BEACH domain reveals an unusual fold and extensive association with a novel PH domain.

The BEACH domain is highly conserved in a large family of eukaryotic proteins, and is crucial for their functions in vesicle trafficking, membrane dynamics and receptor signaling. However, it does not share any sequence homology with other proteins. Here we report the crystal structure at 2.9 A resolution of the BEACH domain of human neurobeachin. It shows that the BEACH domain has a new and unusual polypeptide backbone fold, as the peptide segments in its core do not assume regular secondary structures. Unexpectedly, the structure also reveals that the BEACH domain is in extensive association with a novel, weakly conserved pleckstrin-homology (PH) domain. Consistent with the structural analysis, biochemical studies show that the PH and BEACH domains have strong interactions, suggesting they may function as a single unit. Functional studies in intact cells demonstrate the requirement of both the PH and the BEACH domains for activity. A prominent groove at the interface between the two domains may be used to recruit their binding partners.

Geology and mapping of dark terrain on Ganymede and implications for grooved terrain formation

Geological mapping of regional and high‐resolution Galileo images reveals a variety of units and structures within Ganymede's dark terrain. We have made a detailed study of areas within Galileo, Marius, and Nicholson Regiones in order to investigate the style of tectonic deformation experienced by dark terrain adjacent to swaths of grooved terrain. Dark terrain appears to become fractured as a precursor to grooved terrain formation; in places, dark fractured swaths are recognized which have similar characteristics to brighter grooved terrain swaths. Tectonic deformation may be, but is not always, focused through preexisting weaknesses caused by impact craters and furrows. A prominent groove lane, Anshar Sulcus, is inferred to have formed by the process of hanging wall rollover, accompanied by a small amount of right‐lateral horizontal shear offset resulting from NE‐SW extension.

The 2.8 A crystal structure of Gla-domainless activated protein C.

The structure of the Gla-domainless form of the human anticoagulant enzyme activated protein C has been solved at 2.8 A resolution. The light chain is composed of two domains: an epidermal growth factor (EGF)-like domain modified by a large insert containing an additional disulfide, followed by a typical EGF-like domain. The arrangement of the long axis of these domains describes an angle of approximately 80 degrees. Disulfide linked to the light chain is the catalytic domain, which is generally trypsin-like but contains a large insertion loop at the edge of the active site, a third helical segment, a prominent cationic patch analogous to the anion binding exosite I of thrombin and a trypsin-like Ca[II] binding site. The arrangement of loops around the active site partially restricts access to the cleft. The S2 and S4 subsites are much more polar than in factor Xa and thrombin, and the S2 site is unrestricted. While quite open and exposed, the active site contains a prominent groove, the surface of which is very polar with evidence for binding sites on the primed side, in addition to those typical of the trypsin class found on the non-primed side.

A model and map of Amalthea

A topographic model of Amalthea (JV) was derived from the shapes of limbs and terminators in Voyager images, modified locally to accommodate large craters and ridges. The model is presented in tabular and graphic form, including the first detailed shaded relief maps of the satellite. The shape is very irregular, with radii varying between about 53 and 151 ± 5 km. The minimum value occurs in a deep crater at the south pole. The volume is estimated to be 2.5 ± 0.5 × 106km3. A prominent groove or valley extends some 150 km across the trailing side. High albedo, spectrally distinct markings are mapped and found to have a less obvious relationship with relief than previously suggested.

Reconstitution by MHC-restricted peptides of HLA-A2 heavy chain with β2-microglobulin, in vitro

Cytotoxic T lymphocytes kill virally infected cells when they detect antigenic fragments presented by class I major histocompatibility complex (MHC) antigens (HLA in humans). The crystal structures of HLA-A2 and HLA-Aw68 reveal that peptide-antigen forms an integral part of the HLA structure, being retained in a prominent groove even after purification and crystallization. Here we report that the heavy chain and beta 2-microglobulin of HLA-A2, after separation and fractionation in denaturants, reassemble efficiently under renaturing conditions only in the presence of MHC-restricted peptides. A complex of heavy chain, beta 2-microglobulin, and viral peptide in the ratio 1:1:1 is formed in up to 46% yield. Reconstitution is not stimulated by either of two peptides not restricted to HLA-A2. The reconstituted complex of HLA-A2 and the influenza virus (B/Lee/40) nucleoprotein peptide, Np (85-94), crystallizes under conditions previously used to crystallize HLA-A2. Peptide-linked folding and assembly suggests mechanisms for the unusual capacity of HLA to bind many peptides of diverse sequence.

Impact fracture patterns on phobos ellipsoids

Phobos-ellipsoid models made of clay were fragmented by the impact of high-velocity projectiles to examine the idea proposed by P. Thomas, J. Veverka, and T. Duxbury ((1978) Nature 273, 282–284) that the grooves on Phobos are the manifestation of fractures produced by the Stickney-forming impact. The fracture lines on the models consist of two sets. One is concentric around the impact site and along E lines, which are defined as the intersecting lines of the ellipsoid surface and a set of spherical surfaces with the center of the spheres at the impact site. The other runs radially from the impact site and along P lines, which are defined as the lines crossing E lines perpendicularly on the ellipsoid surface. Some patterns of the grooves originating radially from the crater Stickney on Phobos are very similar to the P lines. The gridded topography, hummocky groove sections, and smooth topography on Phobos could have been formed by the fracture or associated surface disturbances due to the wave induced by the Stickney-forming impact, because they are distributed along the E lines surrounding the converging point of the P lines. All the models except one showed that the density of the fractures east of the impact site is greater than that of those to the west. Fracture patterns similar to one of the most prominent groove sets, which converge and diminish into the region of about (270°, 0°) were not produced by the impact on the ellipsoid of uniform constituent. These grooves would have been produced by the opening of preexisting cracks by the Stickney-forming impact. Other grooves also seem to be affected by such latent cracks.

Cell wall, zoospore and morphological characteristics of Australian isolates of a Pythium causing equine phycomycosis

The asexual and cultural characteristics of a number of Australian isolates of a Pythium causing equine phycomycosis are described. Oospores were not found which precludes positive identification. Zoospores were induced to form after growth in a defined medium. They are ovoid to reniform, biflagellate with flagella arising from a common point within a prominent lateral groove. The groove is overarched by outgrowths from the zoospore. Anterior flagella are of the tinsel type and are shorter than the posterior whiplash flagellum. X-ray diffraction analysis of cell walls failed to demonstrate the presence of cellulose I. Chromatograms of cell wall hydrolysates indicated that glucose is the major component with small contributions being made by mannose, galactose and rhamnose.

The copulatory complex of Hemianax ephippiger (Burmeister) (Aeshnidae: Anisoptera)

Summary Like other Anisoptera Hemianax ephippiger (Burmeister) bears two sets of copulatory apparatuses. The first set which is primary in nature is located on the ventral surface of the ninth abdominal segment and consists of the vestigial penis, the gonocoxites, the supra-anal appendages, the infra-anal appendage. The supra-anal appendages are well developed, lanceolate with serrate margin and spinous apices. They are dorso-ventrally flattened and furnished with long hairs and black teeth-like tubercles (T). The secondary copulatory complex is lodged inside the membranous fossa located on the ventral surface of second and third abdominal segments. It consists of anterior lamina, the posterior lamina, the supporting framework, the hamules, the penis sheath, the penis vesicle and the penis. The anterior lamina is deeply cleft at the posterior margin to accommodate the ovipositor of the female during copulation. Both the portions of the supporting framework are well developed. The anterior portion is somewhat rectangular while the posterior portion is nearly U-shaped. The anterior hamules are well developed with truncated and hooked portions, while the posterior hamules are very much reduced. The penis sheath is forcepate with well developed rectangular flap which hangs over the penis. The penis is stout, clearly demarcated into three segments, and bears a prominent groove on the mid-ventral line.