Portal de Periódicos da CAPES

Paper alert

2001; Elsevier BV; Volume: 9; Issue: 8 Linguagem: Inglês

10.1016/s0969-2126(01)00633-5

1878-4186

Chosen by Robert Liddington, Christin Frederick, Stephen D. Fuller, Sophie Jackson,

A selection of interesting papers that were published in the month before our press date in major journals most likely to report significant results in structural biology, protein and RNA folding. □ Structure of the replicating complex of a Pol α family DNA polymerase. Matthew C. Franklin, Jimin Wang, and Thomas A. Steitz (2001). Cell 105, 657-667. The authors describe the 2.6 Å resolution crystal structure of RB69 DNA polymerase with primer-template DNA and dTTP, capturing the step just before primer extension. This ternary complex structure in the human DNA polymerase α family shows a 60° rotation of the fingers domain relative to the apo-protein structure, similar to the fingers movement in pol I family polymerases. Minor groove interactions near the primer 3′ terminus suggest a common fidelity mechanism for pol I and pol α family polymerases. The duplex product DNA orientation differs by 40° between the polymerizing mode and editing mode structures. The role of the thumb in this DNA motion provides a model for editing in the pol α family. □ Molecular insights into polyubiquitin chain assembly: Crystal structure of the Mms2/Ubc13 heterodimer. Andrew P. VanDemark, Roseanne M. Hofmann, Colleen Tsui, Cecile M. Pickart, and Cynthia Wolberger (2001). Cell 105, 711–720. While the signaling properties of ubiquitin depend on the topology of polyubiquitin chains, little is known concerning the molecular basis of specificity in chain assembly and recognition. UEV/Ubc complexes have been implicated in the assembly of Lys63-linked polyubiquitin chains that act as a novel signal in postreplicative DNA repair and IκBα kinase activation. The crystal structure of the Mms2/Ubc13 heterodimer shows the active site of Ubc13 at the intersection of two channels that are potential binding sites for the two substrate ubiquitins. Mutations that destabilize the heterodimer interface confer a marked UV sensitivity, providing direct evidence that the intact heterodimer is necessary for DNA repair. □ Crystal structure of glycogen synthase kinase 3β: Structural basis for phosphate-primed substrate specificity and autoinhibition. Rana Dajani, Elizabeth Fraser, S. Mark Roe, Neville Young, Valerie Good, Trevor C. Dale, and Laurence H. Pearl (2001). Cell 105, 721–732. Glycogen synthase kinase 3β (GSK3β) plays a key role in insulin and Wnt signaling, phosphorylating downstream targets by default, and becoming inhibited following the extracellular signaling event. The crystal structure of human GSK3β shows a catalytically active conformation in the absence of activation-segment phosphorylation, with the sulphonate of a buffer molecule bridging the activation-segment and N-terminal domain in the same way as the phosphate group of the activation-segment phospho-Ser/Thr in other kinases. The location of this oxyanion binding site in the substrate binding cleft indicates direct coupling of P+4 phosphate-primed substrate binding and catalytic activation, explains the ability of GSK3β to processively hyperphosphorylate substrates with Ser/Thr pentad-repeats, and suggests a mechanism for autoinhibition in which the phosphorylated N terminus binds as a competitive pseudosubstrate with phospho-Ser 9 occupying the P+4 site. □ Structural basis of the interaction of the pyelonephritic E. coli adhesin to its human kidney receptor. Karen W. Dodson, Jerome S. Pinkner, Thierry Rose, Goran Magnusson, Scott J. Hultgren, and Gabriel Waksman (2001). Cell 105, 733–743. PapG is the adhesin at the tip of the P pilus that mediates attachment of uropathogenic E. coli to the uroepithelium of the human kidney. The human specific allele of PapG binds to globoside (GbO4), which consists of the tetrasaccharide GalNAcβ1-3Galα1-4Galβ1-4Glc linked to ceramide. The authors present the crystal structures of a binary complex of the PapG receptor binding domain bound to GbO4 as well as the unbound form of the adhesin. The biological importance of each of the residues involved in binding was investigated by site-directed mutagenesis. These studies provide a molecular snapshot of a host-pathogen interaction that determines the tropism of uropathogenic E. coli for the human kidney and is critical to the pathogenesis of pyelonephritis. □ A structural pathway for activation of the kinesin motor ATPase. Mikyung Yun, Xiaohua Zhang, Cheon-Gil Park, Hee-Won Park, and Sharyn A. Endow (2001). EMBO J. 20, 2611–2618. Molecular motors move along actin or microtubules by rapidly hydrolyzing ATP and undergoing changes in filament-binding affinity with steps of the nucleotide hydrolysis cycle. To identify the conformational changes underlying motor movement on its filament, the authors solved the crystal structures of three kinesin mutants that decouple nucleotide and microtubule binding by the motor and block microtubule-activated, but not basal, ATPase activity. Conformational changes in the structures include a disordered loop and helices in the switch I region and a visible switch II loop, which is disordered in wild-type structures. The structural changes define a signaling pathway within the motor for ATPase activation that is likely to be required for motor movement on microtubules. □ Structure of Golgi-mannosidase II: a target for inhibition of growth and metastasis of cancer cells. Jean M.H. van den Elsen, Douglas A. Kuntz, and David R. Rose (2001). EMBO J. 20, 3008–3017. Golgi-mannosidase II, a key enzyme in N-glycan processing, is a target in the development of anti-cancer therapies. The crystal structure of Drosophila Golgi-mannosidase II in the absence and presence of the anti-cancer agent swainsonine and the inhibitor deoxymannojirimycin reveals a novel protein fold with an active site zinc intricately involved both in the substrate specificity of the enzyme and directly in the catalytic mechanism. Identification of a putative GlcNAc binding pocket in the vicinity of the active site cavity provides a model for the binding of the GlcNAcMan5GlcNAc2 substrate and the consecutive hydrolysis of the 1,6- and 1,3-linked mannose residues. □ The B-box dominates SAP-1–SRF interactions in the structure of the ternary complex. Markus Hassler and Timothy J. Richmond (2001). EMBO J. 20, 3018–3028. The serum response element (SRE) is found in several immediate-early gene promoters. This DNA sequence is necessary and sufficient for rapid transcriptional induction of the human c-fos proto-oncogene in response to stimuli external to the cell. Full activation of the SRE requires the cooperative binding of a ternary complex factor (TCF) and serum response factor (SRF) to their specific DNA sites. The crystal structure of the human SAP-1–SRF–SRE DNA ternary complex shows SAP-1 TCF bound to SRF through interactions between the SAP-1 B-box and SRF MADS domain in addition to contacts between their respective DNA-binding motifs. The SAP-1 B-box is part of a flexible linker of which 21 amino acids become ordered upon ternary complex formation. □ Structure of a pilin monomer from Pseudomonas aeruginosa: Implications for the assembly of pili. David W. Keizer, Carolyn M. Slupsky, Michal Kalisiak, A. Patricia Campbell, Matthew P. Crump, Parimi A. Sastry, Bart Hazes, Randall T. Irvin, and Brian D. Sykes (2001). J. Biol. Chem. 276, 24186–24193. Type IV pilin monomers assemble to form fibers called pili that are required for a variety of bacterial functions. Pilin monomers oligomerize due to the interaction of part of their hydrophobic N-terminal α-helix. Engineering of a truncated pilin from Pseudomonas aeruginosa where the first 28 residues are removed from the N terminus yields a soluble, monomeric protein. This truncated pilin binds to its receptor and decreases morbidity and mortality in mice before challenge with a heterologous strain of Pseudomonas. The structure consists of an α-helix at the N terminus that lies across a four-stranded antiparallel β-sheet. A model for a pilus is proposed that takes into account both electrostatic and hydrophobic interactions of pilin subunits as well as previously published X-ray fiber diffraction data. The model indicates that DNA or RNA cannot pass through the center of the pilus, while small organic molecules may, suggesting a mechanism for signal transduction. □ Incorporation of β-selenolo[3,2-b]pyrrolyl-alanine into proteins for phase determination in protein X-ray crystallography. Jae Hyun Bae, Stefan Alefelder, Jens T. Kaiser, Rainer Friedrich, Luis Moroder, Robert Huber, and Nediljko Budisa (2001). J. Mol. Biol. 309, 925-936. Published online as 10.1006/jmbi.2001.4699. β-selenolo[3,2-b]pyrrolyl-L-alanine mimics tryptophan, with the benzene ring of the indole moiety replaced by selenophene. This was incorporated into human annexin V and barstar using a Trp-auxotrophic Escherichia coli host strain. The seleno-proteins were obtained in yields comparable to those of the wild-type proteins and exhibit full crystallographic isomorphism to the parent proteins and the possibility of MAD phasing. □ FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. Jiye Shi, Tom L. Blundell, and Kenji Mizuguchi (2001). J. Mol. Biol. 310, 243–257. Published online as 10.1006/jmbi.2001.4762. FUGUE, a program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three key features. (1) Improved environment-specific substitution tables. (2) Automatic selection of alignment algorithm with detailed structure-dependent gap penalties. (3) Combined information from both multiple sequences and multiple structures. The combination of these three key features implemented in FUGUE improves both homology recognition performance and alignment accuracy. □ An extended RNA binding surface through arrayed S1 and KH domains in transcription factor NusA. Michael Worbs, Gleb P. Bourenkov, Hans D. Bartunik, Robert Huber, and Markus C. Wahl (2001). Mol. Cell 7, 1177–1189. The crystal structure of Thermotoga maritima NusA, a transcription factor involved in pausing, termination, and antitermination processes, reveals a four-domain, rod-shaped molecule. An N-terminal α/β portion, a five-stranded β-barrel (S1 domain), and two K-homology (KH) modules create a continuous spine of positive electrostatic potential, suitable for nonspecific mRNA attraction. Homology models suggest how, in addition, specific mRNA regulatory sequences can be recognized by the S1 and KH motifs. An arrangement of multiple S1 and KH domains mediated by highly conserved residues is seen, creating an extended RNA binding surface, a paradigm for other proteins with similar domain arrays. Structural and mutational analyses indicate that the motifs cooperate, modulating strength and specificity of RNA binding. □ Potassium channel receptor site for the inactivation gate and quaternary amine inhibitors. Ming Zhou, João H. Morais-Cabral, Sabine Mann, and Roderick MacKinnon (2001). Nature 411, 657–661. Many voltage-dependent K+ channels open when the membrane is depolarized and then rapidly close by a process called inactivation. Neurons use inactivating K+ channels to modulate their firing frequency. In Shaker-type K+ channels, the inactivation gate, which is responsible for the closing of the channel, is formed by the channel's cytoplasmic amino terminus. Here, the authors show that the central cavity and inner pore of the K+ channel form the receptor site for both the inactivation gate and small-molecule inhibitors. They propose that inactivation occurs by a sequential reaction in which the gate binds initially to the cytoplasmic channel surface and then enters the pore as an extended peptide. □ Structure of a human T-cell antigen receptor. Timothy J. Allison, Christine C. Winter, Jean-Jacques Fournié, Marc Bonneville, and David N. Garboczi (2001). Nature 411, 820–824. T-cell antigen receptors composed of γ and δ polypeptide chains (γδTCRs) can directly recognize antigens in the form of intact proteins or non-peptide compounds, unlike αβTCRs, which recognize antigens bound to major histocompatibility complex molecules (MHC). About 5% of peripheral blood T cells bear TCRs, most of which recognize non-peptide phosphorylated antigens. Here the crystal structure of a human γδTCR from a T-cell clone that is phosphoantigen-reactive is described. The orientation of the variable (V) and constant (C) regions of the γδTCR is unique and results from an unusually small angle between the Vγ and Cγ domains. The complementarity-determining regions (CDRs) of the Vγ domains display a likely binding site for phosphorylated antigens. The Cγ domains are markedly different, which may enable γδTCRs to form different recognition/signaling complexes than αβTCRs. □ Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution. Patrick Jordan, Petra Fromme, Horst Tobias Witt, Olaf Klukas, Wolfram Saenger, and Norbert Krau (2001). Nature 411, 909–917. In plants, green algae and cyanobacteria, photosynthesis is driven by the cooperation of two large protein–cofactor complexes, photosystems I and II, which are located in the thylakoid membranes. The crystal structure of photosystem I from the thermophilic cyanobacterium Synechococcus elongatus described here provides a picture in atomic detail of 12 protein subunits and 127 cofactors comprising 96 chlorophylls, 2 phylloquinones, 3 Fe4S4 clusters, 22 carotenoids, 4 lipids, a putative Ca2+ ion, and 201 water molecules. The structural information on the proteins and cofactors and their interactions provides a basis for understanding how the high efficiency of photosystem I in light capturing and electron transfer is achieved. □ Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Anita Changela, Russell J. Digate, and Alfonso Mondragón (2001). Nature 411, 1077–1081. DNA topoisomerase III from E. coli belongs to the type IA family of DNA topoisomerases, which transiently cleave ssDNA via formation of a covalent 5′ phosphotyrosine intermediate. The crystal structure of an inactive mutant of E. coli DNA topoisomerase III in complex with an 8-base ssDNA molecule shows that the enzyme undergoes a conformational change that allows the oligonucleotide to bind within a groove leading to the active site. The structure rationalizes the role of several highly conserved residues during catalysis, with functional implications for other topoisomerases and proteins that perform DNA rearrangements. □ Implications for familial hypercholesterolemia from the structure of the LDL receptor YWTD-EGF domain pair. H. Jeon, W. Meng, J. Takagi, M.J. Eck, T.A. Springer, and S.C. Blacklow (2001). Nat. Struct. Biol. 8, 499–504. The low-density lipoprotein receptor (LDLR) is the primary mechanism for uptake of cholesterol-carrying particles into cells. The region of the LDLR implicated in receptor recycling and lipoprotein release at low pH contains a pair of calcium-binding EGF-like modules, followed by a series of six YWTD repeats and a third EGF-like module. The crystal structure at 1.5 Å resolution of a receptor fragment spanning the YWTD repeats and its two flanking EGF modules reveals that the YWTD repeats form a six-bladed β-propeller that packs tightly against the C-terminal EGF module, whereas the EGF module that precedes the propeller is disordered in the crystal. Numerous point mutations of the LDLR that result in the genetic disease familial hypercholesterolemia (FH) alter side chains that form conserved packing and hydrogen bonding interactions in the interior and between propeller blades. A second subset of FH mutations are located at the interface between the propeller and the C-terminal EGF module, suggesting a structural requirement for maintaining the integrity of the interdomain interface. □ An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images. Jianwei Miao, Keith O. Hodgson, and David Sayre (2001). Proc. Natl. Acad. Sci. USA 98, 6641–6645. The authors describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense X-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5 Å resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level X-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. □ Antigen presentation subverted: Structure of the human cytomegalovirus protein US2 bound to the class I molecule HLA-A2. Benjamin E. Gewurz, Rachelle Gaudet, Domenico Tortorella, Evelyn W. Wang, Hidde L. Ploegh, and Don C. Wiley (2001). Proc. Natl. Acad. Sci. USA 98, 6794–6799. Many persistent viruses have evolved the ability to subvert MHC class I antigen presentation by down-regulating cell-surface expression of class I. The human cytomegalovirus (HCMV) unique short (US)2 glycoprotein binds newly synthesized class I molecules within the endoplasmic reticulum (ER) and subsequently targets them for proteasomal degradation. The authors report the crystal structure of US2 bound to the HLA-A2/Tax peptide complex. US2 associates with HLA-A2 at the junction of the peptide-binding region and the α3 domain, a novel binding surface on class I that allows US2 to bind independently of peptide sequence. Mutation of class I heavy chains confirms the importance of this binding site in vivo. □ Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae. Martin Sagermann, Tom H. Stevens, and Brian W. Matthews (2001). Proc. Natl. Acad. Sci. USA 98, 7134–7139. In contrast to the F-type ATPases, which use a proton gradient to generate ATP, the V-type enzymes use ATP to actively transport protons into organelles and extracellular compartments. The authors describe the structure of the H-subunit (also called Vma13p) of the yeast enzyme. This is the first structure of any component of a V-type ATPase. The H-subunit is not required for assembly but plays an essential regulatory role. Despite the lack of any apparent sequence homology, the structure contains five motifs similar to the so-called HEAT or armadillo repeats seen in the importins. A groove, which is occupied in the importins by the peptide that targets proteins for import into the nucleus, is occupied here by the 10 amino-terminal residues of subunit H itself. □ Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X. Hiroshi Mizuno, Zui Fujimoto, Hideko Atoda, and Takashi Morita (2001). Proc. Natl. Acad. Sci. USA 98, 7230–7234. Published online before print as 10.1073/PNAS.131179698 The γ-carboxyglutamic acid (Gla) domain of blood coagulation factors is responsible for Ca2+-dependent phospholipid membrane binding. Factor X-binding protein (X-bp), an anticoagulant protein from snake venom, specifically binds to the Gla domain of factor X. The crystal structure of X-bp in complex with the Gla domain peptide of factor X at 2.3 Å resolution showed that the anticoagulation is based on the fact that two patches of the Gla domain essential for membrane binding are buried in the complex formation. This structure also provides a membrane-bound model of factor X. □ Structure of complement receptor 2 in complex with its C3d ligand. Gerda Szakonyi, Joel M. Guthridge, Dawei Li, Kendra Young, V. Michael Holers, Xiaojiang S. Chen (2001). Science 292, 1725–1728. Complement receptor 2 (CR2/CD21) is an important receptor that amplifies B lymphocyte activation by bridging the innate and adaptive immune systems. CR2 ligands include complement C3d and Epstein-Barr virus glycoprotein 350/220. The authors describe the x-ray structure of this CR2 domain in complex with C3d at 2.0 Å. The structure reveals extensive main chain interactions between C3d and only one short consensus repeat (SCR) of CR2 and substantial SCR side-side packing. These results provide a detailed understanding of receptor-ligand interactions in this protein. □ Structural basis of transcription: RNA polymerase II at 2.8 Å resolution. Patrick Cramer, David A. Bushnell, and Roger D. Kornberg (2001). Science 292, 1863–1876. Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 Å resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 Å structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 Å difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain. □ Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 Å resolution. Averell L. Gnatt, Patrick Cramer, Jianhua Fu, David A. Bushnell, and Roger D. Kornberg (2001). Science 292, 1876–1882. The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 Å resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 3′ end of the RNA in the nucleotide addition site. The 3′ end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 5′-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of “switches” at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. □ A structural genomics approach to the study of quorum sensing: Crystal structures of three LuxS orthologs. Hal A. Lewis, Eva Bric Furlong, Boris Laubert, Galina A. Eroshkina, Yelena Batiyenko, Jason M. Adams, Mark G. Bergseid, Curtis D. Marsh, Thomas S. Peat, Wendy E. Sanderson, J. Michael Sauder, and Sean G. Buchanan (2001). Structure 9, 527–537. Quorum sensing is the mechanism by which bacteria control gene expression in response to cell density. The luxS gene is required for the AI-2 system of quorum sensing, which is involved in the expression of virulence genes in several pathogens. The crystal structures of the LuxS protein from three different bacterial species have been solved using an X-ray crystallographic structural genomics approach, revealing a new homo-dimeric alpha-beta fold. A metal ion identified as zinc was seen bound to a Cys-His-His triad. These structures provide support for a hypothesis in which the protein binds a methionine analog, S-ribosylhomocysteine (SRH). The zinc atom is in position to cleave the ribose ring in a step along the synthesis pathway of AI-2.