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Structure (v.18, #1)

In This Issue (pp. ix-x).

Convergent Recognition of a Triple Helical Hydrophobic Motif in Collagen by Jonas Emsley (pp. 1-2).
Principal receptors for collagen, the most abundant component of the extracellular matrix (ECM), come from the integrin and discoidin domain (DDR) gene families. The latter are a class of receptor tyrosine kinases that bind to several collagens and mediate intracellular signaling. Carafoli et al. recently described a crystal structure of a DDR in complex with a trimeric collagen peptide ligand.

Herpesviruses: An In-Depth View by Frazer J. Rixon (pp. 2-4).
Transmission electron microscopy of thin sections is the primary means for visualizing structures within cells. In this issue of Structure, Peng et al. extend this approach by using electron tomography to examine the life cycle of a herpesvirus and provide fresh insights into the processes of DNA packaging and release.

Molecular Machines and Targeted Molecular Dynamics: DNA in Motion by Janice D. Pata; Joachim Jaeger (pp. 4-6).
In this issue of Structure, Golosov et al. present molecular dynamics simulations that illuminate the process of DNA translocation by an A-family DNA polymerase. Several distinct phases are identified that have not been visualized through crystallographic studies.

Catching Pneumonia by Robert Liddington (pp. 6-8).
Many Gram-positive bacteria have pili attached to their cell walls, but they are much simpler and shorter than their more familiar Gram-negative analogs. The structure of an “adhesin” from the tip of the pneumococcal pilus () reveals intradomain insertions of eukaryotic origin that may hold the key to systemic invasion.

Reverse Micelle Encapsulation of Membrane-Anchored Proteins for Solution NMR Studies by Kathleen G. Valentine; Ronald W. Peterson; Jamil S. Saad; Michael F. Summers; Xianzhong Xu; James B. Ames; A. Joshua Wand (pp. 9-16).
Perhaps 5%–10% of proteins bind to membranes via a covalently attached lipid. Posttranslational attachment of fatty acids such as myristate occurs on a variety of viral and cellular proteins. High-resolution information about the nature of lipidated proteins is remarkably sparse, often because of solubility problems caused by the exposed fatty acids. Reverse micelle encapsulation is used here to study two myristoylated proteins in their lipid-extruded states: myristoylated recoverin, which is a switch in the Ca2+ signaling pathway in vision, and the myristoylated HIV-1 matrix protein, which is postulated to be targeted to the plasma membrane through its binding to phosphatidylinositol-4,5-bisphosphate. Both proteins have been successfully encapsulated in the lipid-extruded state and high-resolution NMR spectra obtained. Both proteins bind their activating ligands in the reverse micelle. This approach seems broadly applicable to membrane proteins with exposed fatty acid chains that have eluded structural characterization by conventional approaches.Display Omitted► Reverse micelle encapsulation technology has been applied to myristoylated proteins► Excellent solution NMR spectra of encapsulated myristoylated proteins are obtained ► Encapsulated myristoylated recoverin and HIV-1 matrix protein are in the lipid-extruded state ► The HIV-1 matrix protein binding site for PI(4,5)P2 can be directly determined

Keywords: PROTEINS


Zernike Phase Plate Cryoelectron Microscopy Facilitates Single Particle Analysis of Unstained Asymmetric Protein Complexes by Wei-Hau Chang; Michael T.-K. Chiu; Chin-Yu Chen; Chi-Fu Yen; Yen-Cheng Lin; Yi-Ping Weng; Ji-Chau Chang; Yi-Min Wu; Holland Cheng; Jianhua Fu; I-Ping Tu (pp. 17-27).
Single particle reconstruction from cryoelectron microscopy images, though emerging as a powerful means in structural biology, is faced with challenges as applied to asymmetric proteins smaller than megadaltons due to low contrast. Zernike phase plate can improve the contrast by restoring the microscope contrast transfer function. Here, by exploiting simulated Zernike and conventional defocused cryoelectron microscope images with noise characteristics comparable to those of experimental data, we quantified the efficiencies of the steps in single particle analysis of ice-embedded RNA polymerase II (500 kDa), transferrin receptor complex (290 kDa), and T7 RNA polymerase lysozyme (100 kDa). Our results show Zernike phase plate imaging is more effective as to particle identification and also sorting of orientations, conformations, and compositions. Moreover, our analysis on image alignment indicates that Zernike phase plate can, in principle, reduce the number of particles required to attain near atomic resolution by 10–100 fold for proteins between 100 kDa and 500 kDa.

Keywords: PROTEINS


Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces by Shivender M.D. Shandilya; Madhavi N.L. Nalam; Ellen A. Nalivaika; Phillip J. Gross; Johnathan C. Valesano; Keisuke Shindo; Ming Li; Mary Munson; William E. Royer; Elena Harjes; Takahide Kono; Hiroshi Matsuo; Reuben S. Harris; Mohan Somasundaran; Celia A. Schiffer (pp. 28-38).
APOBEC3G is a DNA cytidine deaminase that has antiviral activity against HIV-1 and other pathogenic viruses. In this study the crystal structure of the catalytically active C-terminal domain was determined to 2.25 Å. This structure corroborates features previously observed in nuclear magnetic resonance (NMR) studies, a bulge in the second β strand and a lengthening of the second α helix. Oligomerization is postulated to be critical for the function of APOBEC3G. In this structure, four extensive intermolecular interfaces are observed, suggesting potential models for APOBEC3G oligomerization. The structural and functional significance of these interfaces was probed by solution NMR and disruptive variants were designed and tested for DNA deaminase and anti-HIV activities. The variant designed to disrupt the most extensive interface lost both activities. NMR solution data provides evidence that another interface, which coordinates a novel zinc site, also exists. Thus, the observed crystallographic interfaces of APOBEC3G may be important for both oligomerization and function.

Keywords: PROTEINS; DNA


Probing the Interactions of Carboxy-atractyloside and Atractyloside with the Yeast Mitochondrial ADP/ATP Carrier by Alexej Kedrov; Alex M. Hellawell; Adam Klosin; R. Bill Broadhurst; Edmund R.S. Kunji; Daniel J. Müller (pp. 39-46).
Mitochondrial ADP/ATP carriers are inhibited by two natural compounds, atractyloside (ATR) or carboxy-atractyloside (CATR), which differ by one carboxylate group. The interactions of the inhibitors with the carrier were investigated by single-molecule force spectroscopy. Transmembrane α helices of the ATR-inhibited carrier displayed heterogeneous mechanical and kinetic properties. Whereas α helix H2 showed the most brittle mechanical properties and lowest kinetic stability, α helix H5 was mechanically the most flexible and possessed a kinetic stability 9 orders of magnitude greater than that of α helix H2. In contrast, CATR-binding substantially increased the kinetic stability of α helix H2 and tuned the mechanical flexibility of α helices H5 and H6. NMR spectroscopy confirmed that the additional carboxylate group of CATR binds to the sixth α helix, indicating that the enhanced stability of H2 is mediated via interactions between CATR and H6.Display Omitted

Keywords: PROTEINS


Three-Dimensional Visualization of Gammaherpesvirus Life Cycle in Host Cells by Electron Tomography by Li Peng; Sergey Ryazantsev; Ren Sun; Z. Hong Zhou (pp. 47-58).
Gammaherpesviruses are etiologically associated with human tumors. A three-dimensional (3D) examination of their life cycle in the host is lacking, significantly limiting our understanding of the structural and molecular basis of virus-host interactions. Here, we report the first 3D visualization of key stages of the murine gammaherpesvirus 68 life cycle in NIH 3T3 cells, including viral attachment, entry, assembly, and egress, by dual-axis electron tomography. In particular, we revealed the transient processes of incoming capsids injecting viral DNA through nuclear pore complexes and nascent DNA being packaged into progeny capsids in vivo as a spool coaxial with the putative portal vertex. We discovered that intranuclear invagination of both nuclear membranes is involved in nuclear egress of herpesvirus capsids. Taken together, our results provide the structural basis for a detailed mechanistic description of gammaherpesvirus life cycle and also demonstrate the advantage of electron tomography in dissecting complex cellular processes of viral infection.

Keywords: MICROBIO


A TNF-like Trimeric Lectin Domain from Burkholderia cenocepacia with Specificity for Fucosylated Human Histo-Blood Group Antigens by Ondřej Šulák; Gianluca Cioci; Monia Delia; Martina Lahmann; Annabelle Varrot; Anne Imberty; Michaela Wimmerová (pp. 59-72).
The opportunistic pathogen Burkholderia cenocepacia expresses several soluble lectins, among them BC2L-C. This lectin exhibits two domains: a C-terminal domain with high sequence similarity to the recently described calcium-dependent mannose-binding lectin BC2L-A, and an N-terminal domain of 156 amino acids without similarity to any known protein. The recombinant N-terminal BC2L-C domain is a new lectin with specificity for fucosylated human histo-blood group epitopes H-type 1, Lewis b, and Lewis Y, as determined by glycan array and isothermal titration calorimetry. Methylselenofucoside was used as ligand to solve the crystal structure of the N-terminal BC2L-C domain. Additional molecular modeling studies rationalized the preference for Lewis epitopes. The structure reveals a trimeric jellyroll arrangement with striking similarity to TNF-like proteins, and to BclA, the spore protein from Bacillus anthracis which may play an important role in bioadhesion of anthrax spores in human lungs.

Solution Structure of a Unique G-Quadruplex Scaffold Adopted by a Guanosine-Rich Human Intronic Sequence by Vitaly Kuryavyi; Dinshaw J. Patel (pp. 73-82).
We report on the solution structure of an unprecedented intramolecular G-quadruplex formed by the guanosine-rich human chl1 intronic d(G3-N-G4-N2-G4-N-G3-N) 19-mer sequence in K+-containing solution. This G-quadruplex, composed of three stacked G-tetrads containing four syn guanines, represents a new folding topology with two unique conformational features. The first guanosine is positioned within the central G-tetrad, in contrast to all previous structures of unimolecular G-quadruplexes, where the first guanosine is part of an outermost G-tetrad. In addition, a V-shaped loop, spanning three G-tetrad planes, contains no bridging nucleotides. The G-quadruplex scaffold is stabilized by a T•G•A triple stacked over the G-tetrad at one end and an unpaired guanosine stacked over the G-tetrad at the other end. Finally, the c hl1 intronic DNA G-quadruplex scaffold contains a guanosine base intercalated between an extended G-G step, a feature observed in common with the catalytic site of group I introns. This unique structural scaffold provides a highly specific platform for the future design of ligands specifically targeted to intronic G-quadruplex platforms.

Keywords: DNA


The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis by Andrei A. Golosov; Joshua J. Warren; Lorena S. Beese; Martin Karplus (pp. 83-93).
High-fidelity DNA polymerases copy DNA rapidly and accurately by adding correct deoxynucleotide triphosphates to a growing primer strand of DNA. Following nucleotide incorporation, a series of conformational changes translocate the DNA substrate by one base pair step, readying the polymerase for the next round of incorporation. Molecular dynamics simulations indicate that the translocation consists globally of a polymerase fingers-opening transition, followed by the DNA displacement and the insertion of the template base into the preinsertion site. They also show that the pyrophosphate release facilitates the opening transition and that the universally conserved Y714 plays a key role in coupling polymerase opening to DNA translocation. The transition involves several metastable intermediates in one of which the O helix is bent in the vicinity of G711. Completion of the translocation appears to require a gating motion of the O1 helix, perhaps facilitated by the presence of G715. These roles are consistent with the high level of conservation of Y714 and the two glycine residues at these positions. It is likely that a corresponding mechanism is applicable to other polymerases.

Keywords: DNA


Crystal Structures of Dehydratase Domains from the Curacin Polyketide Biosynthetic Pathway by David L. Akey; Jamie R. Razelun; Jason Tehranisa; David H. Sherman; William H. Gerwick; Janet L. Smith (pp. 94-105).
Modular polyketide synthases (PKS) make novel natural products through a series of preprogrammed chemical steps catalyzed by an assembly line of multidomain modules. Each assembly-line step involves unique extension and modification reactions, resulting in tremendous diversity of polyketide products. Dehydratase domains catalyze formation of an α,β-double bond in the nascent polyketide intermediate. We present crystal structures of the four dehydratase domains from the curacin A PKS. The catalytic residues and substrate binding site reside in a tunnel within a single monomer. The positions of the catalytic residues and shape of the substrate tunnel explain how chirality of the substrate hydroxyl group may determine the configuration of the product double bond. Access to the active site may require opening the substrate tunnel, forming an open trench. The arrangement of monomers within the dimer is consistent among PKS dehydratases and differs from that seen in the related mammalian fatty acid synthases.► Active site location at sharp bend within a tunnel explains how substrate stereochemistry can determine product conformation ► Access to active site is likely mediated by movement of specific structural elements, opening the substrate tunnel to accommodate bulky and/or inflexible substrates ► Re-annotation of Curacin A biosynthetic pathway suggests dehydration reactions may occur across module boundaries ► Orientation of dehydratase monomers in PKS modules differs from that seen for FAS modules but is nonetheless consistent with overall shared architecture of PKS and FAS modules.

Keywords: PROTEINS


Structural Basis of Host Cell Recognition by the Pilus Adhesin from Streptococcus pneumoniae by Thierry Izoré; Carlos Contreras-Martel; Lamya El Mortaji; Clothilde Manzano; Rémy Terrasse; Thierry Vernet; Anne Marie Di Guilmi; Andréa Dessen (pp. 106-115).
Pili are fibrous virulence factors associated directly to the bacterial surface that play critical roles in adhesion and recognition of host cell receptors. The human pathogen Streptococcus pneumoniae carries a single pilus-related adhesin (RrgA) that is key for infection establishment and provides protection from bacterial challenge in animal infection models, but details of these roles remain unclear. Here we report the high-resolution crystal structure of RrgA, a 893-residue elongated macromolecule whose fold contains four domains presenting both eukaryotic and prokaryotic origins. RrgA harbors an integrin I collagen-recognition domain decorated with two inserted “arms” that fold into a positively charged cradle, as well as three “stalk-forming” domains. We show by site-specific mutagenesis, mass spectrometry, and thermal shift assays that intradomain isopeptide bonds play key roles in stabilizing RrgA's stalk. The high sequence similarity between RrgA and its homologs in other Gram-positive microorganisms suggests common strategies for ECM recognition and immune evasion.

Keywords: MICROBIO; PROTEINS


Conformational Changes in Guanylate Cyclase-Activating Protein 1 Induced by Ca2+ and N-Terminal Fatty Acid Acylation by Tivadar Orban; Grzegorz Bereta; Masaru Miyagi; Benlian Wang; Mark R. Chance; Marcelo Carlos Sousa; Krzysztof Palczewski (pp. 116-126).
Neuronal Ca2+ sensors (NCS) are high-affinity Ca2+-binding proteins critical for regulating a vast range of physiological processes. Guanylate cyclase-activating proteins (GCAPs) are members of the NCS family responsible for activating retinal guanylate cyclases (GCs) at low Ca2+ concentrations, triggering synthesis of cGMP and recovery of photoreceptor cells to the dark-adapted state. Here we use amide hydrogen-deuterium exchange and radiolytic labeling, and molecular dynamics simulations to study conformational changes induced by Ca2+ and modulated by the N-terminal myristoyl group. Our data on the conformational dynamics of GCAP1 in solution suggest that Ca2+ stabilizes the protein but induces relatively small changes in the domain structure; however, loss of Ca+2 mediates a significant global relaxation and movement of N- and C-terminal domains. This model and the previously described “calcium-myristoyl switch” proposed for recoverin indicate significant diversity in conformational changes among these highly homologous NCS proteins with distinct functions.Display Omitted

Keywords: PROTEIN; SIGNALING; CELLBIO


Insights from the Structure of a Smallpox Virus Topoisomerase-DNA Transition State Mimic by Kay Perry; Young Hwang; Frederic D. Bushman; Gregory D. Van Duyne (pp. 127-137).
Poxviruses encode their own type IB topoisomerases (TopIBs), which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed by viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single-molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves an Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small versus large enzyme subfamilies.

Keywords: DNA; PROTEINS


Crystal Structure of UbcH5b∼Ubiquitin Intermediate: Insight into the Formation of the Self-Assembled E2∼Ub Conjugates by Eri Sakata; Tadashi Satoh; Shunsuke Yamamoto; Yoshiki Yamaguchi; Maho Yagi-Utsumi; Eiji Kurimoto; Keiji Tanaka; Soichi Wakatsuki; Koichi Kato (pp. 138-147).
E2 ubiquitin-conjugating enzymes catalyze the attachment of ubiquitin to lysine residues of target proteins. The UbcH5b E2 enzyme has been shown to play a key role in the initiation of the ubiquitination of substrate proteins upon action of several E3 ligases. Here we have determined the 2.2 Å crystal structure of an intermediate of UbcH5b∼ubiquitin (Ub) conjugate, which is assembled into an infinite spiral through the backside interaction. This active complex may provide multiple E2 active sites, enabling efficient ubiquitination of substrates. Indeed, biochemical assays support a model in which the self-assembled UbcH5b∼Ub can serve as a bridge for the gap between the lysine residue of the substrate and the catalytic cysteine of E2.Display Omitted

Keywords: PROTEINS

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