Genomes and Genes
Experts and Doctors on x ray crystallography in Toronto, Ontario, Canada
Locale: Toronto, Ontario, Canada
Topic: x ray crystallography
- El Bakkouri M, Pow A, Mulichak A, Cheung K, Artz J, Amani M, et al. The Clp chaperones and proteases of the human malaria parasite Plasmodium falciparum. J Mol Biol. 2010;404:456-77 pubmed publisher..Our data suggest the presence of a ClpCRP complex in the apicoplast of P. falciparum...
- Tsai M, Koo J, Yip P, Colman R, Segall M, Howell P. Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism. J Mol Biol. 2007;370:541-54 pubmed..This loop movement has been observed in other superfamily enzymes, and has been proposed to be essential for catalysis. The ADL catalytic mechanism is re-examined in light of the results presented here. ..
- Whitney J, Neculai A, Ohman D, Howell P. Expression, refolding, crystallization and preliminary X-ray analysis of Pseudomonas aeruginosa AlgE. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:463-6 pubmed publisher..The crystals exhibited the symmetry of space group C222 and diffracted to a minimum d-spacing of 3.0 A. On the basis of the Matthews coefficient (V(M) = 3.28 A(3) Da(-1)), one molecule is estimated to be present in the asymmetric unit...
- Viola C, Saridakis V, Christendat D. Crystal structure of chorismate synthase from Aquifex aeolicus reveals a novel beta alpha beta sandwich topology. Proteins. 2004;54:166-9 pubmed
- Orlicky S, Tang X, Willems A, Tyers M, Sicheri F. Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase. Cell. 2003;112:243-56 pubmed..These features account for the observed phosphorylation threshold in Sic1 recognition and suggest an equilibrium binding mode between a single receptor site in Cdc4 and multiple low-affinity CPD sites in Sic1. ..
- Saridakis V, Shahinas D, Xu X, Christendat D. Structural insight on the mechanism of regulation of the MarR family of proteins: high-resolution crystal structure of a transcriptional repressor from Methanobacterium thermoautotrophicum. J Mol Biol. 2008;377:655-67 pubmed publisher..Electrophoretic mobility shift assay and biophysical analyses further suggest that salicylate inactivates MTH313 and prevents it from binding to its promoter region...
- Savchenko A, Yee A, Khachatryan A, Skarina T, Evdokimova E, Pavlova M, et al. Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches. Proteins. 2003;50:392-9 pubmed
- Gordon R, Sivarajah P, Satkunarajah M, Ma D, Tarling C, Vizitiu D, et al. X-ray crystal structures of rabbit N-acetylglucosaminyltransferase I (GnT I) in complex with donor substrate analogues. J Mol Biol. 2006;360:67-79 pubmed
- Lemke C, Howell P. Substrate induced conformational changes in argininosuccinate synthetase. J Biol Chem. 2002;277:13074-81 pubmed..Combined, these structures also provide structural explanations of some of the observed kinetic properties of the enzyme and have enabled a detailed enzymatic mechanism of AS catalysis to be proposed. ..
- Bosanac I, Michikawa T, Mikoshiba K, Ikura M. Structural insights into the regulatory mechanism of IP3 receptor. Biochim Biophys Acta. 2004;1742:89-102 pubmed..This review aims to provide comprehensive overview of the current information available on the structure and function relationship of IP(3)R. ..
- Lalor D, Schnyder T, Saridakis V, Pilloff D, Dong A, Tang H, et al. Structural and functional analysis of a truncated form of Saccharomyces cerevisiae ATP sulfurylase: C-terminal domain essential for oligomer formation but not for activity. Protein Eng. 2003;16:1071-9 pubmed..Careful inspection and modeling revealed that the groove is sufficiently deep and wide, as well as properly positioned, to act as a substrate channel between the ATP sulfurylase and APS kinase-like domains of the enzyme. ..
- Savchenko A, Skarina T, Evdokimova E, Watson J, Laskowski R, Arrowsmith C, et al. X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution. Proteins. 2004;54:162-5 pubmed
- Turner M, Yuan C, Borchardt R, Hershfield M, Smith G, Howell P. Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength. Nat Struct Biol. 1998;5:369-76 pubmed..An unusual dual role for a catalytic water molecule in the active site is revealed in the complex with the adenosine analog 2'-hydroxy, 3'-ketocyclopent-4'-enyladenine. ..
- Christendat D, Saridakis V, Dharamsi A, Bochkarev A, Pai E, Arrowsmith C, et al. Crystal structure of dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase from Methanobacterium thermoautotrophicum complexed with dTDP. J Biol Chem. 2000;275:24608-12 pubmed publisher..The conservation of the active site residues suggests that the mechanism of action is also conserved and that the RmlC structure may be useful in guiding the design of antibacterial drugs...
- Kuntz D, Zhong W, Guo J, Rose D, Boons G. The molecular basis of inhibition of Golgi alpha-mannosidase II by mannostatin A. Chembiochem. 2009;10:268-77 pubmed publisher..The various structures indicate that differences in the hydration of protein-ligand complexes are also important determinants of plasticity as well as selectivity of inhibitor binding. ..
- Brown G, Singer A, Lunin V, Proudfoot M, Skarina T, Flick R, et al. Structural and biochemical characterization of the type II fructose-1,6-bisphosphatase GlpX from Escherichia coli. J Biol Chem. 2009;284:3784-92 pubmed publisher..Our data provide insight into the molecular mechanisms of the substrate specificity and catalysis of GlpX and other class II fructose-1,6-bisphosphatases. ..
- Tong Y, Tempel W, Nedyalkova L, MacKenzie F, Park H. Crystal structure of the N-acetylmannosamine kinase domain of GNE. PLoS ONE. 2009;4:e7165 pubmed publisher..Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1. ..
- Lee J, Cornell K, Riscoe M, Howell P. Expression, purification, crystallization and preliminary X-ray analysis of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. Acta Crystallogr D Biol Crystallogr. 2001;57:150-2 pubmed..On the basis of density calculations, two monomers are predicted per asymmetric unit (Matthews coefficient, V(M) = 2.37 A(3) Da(-1)), with a solvent content of 48%. ..
- Kuznetsova E, Xu L, Singer A, Brown G, Dong A, Flick R, et al. Structure and activity of the metal-independent fructose-1,6-bisphosphatase YK23 from Saccharomyces cerevisiae. J Biol Chem. 2010;285:21049-59 pubmed publisher..Thus, YK23 represents the first family of metal-independent FBPases and a second FBPase family in eukaryotes. ..
- Avvakumov G, Walker J, Xue S, Finerty P, MacKenzie F, Newman E, et al. Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8). J Biol Chem. 2006;281:38061-70 pubmed..The presence of a zinc ribbon subdomain near the ubiquitin binding site further suggests a polyubiquitin-specific binding site and a mechanism for substrate induced conformational changes. ..
- Wiesner S, Wybenga Groot L, Warner N, Lin H, Pawson T, Forman Kay J, et al. A change in conformational dynamics underlies the activation of Eph receptor tyrosine kinases. EMBO J. 2006;25:4686-96 pubmed
- Sprangers R, Kay L. Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature. 2007;445:618-22 pubmed..Our results establish that NMR spectroscopy can provide detailed insight into supra-molecular structures over an order of magnitude larger than those routinely studied using methodology that is generally applicable...
- Aviv T, Amborski A, Zhao X, Kwan J, Johnson P, Sicheri F, et al. The NMR and X-ray structures of the Saccharomyces cerevisiae Vts1 SAM domain define a surface for the recognition of RNA hairpins. J Mol Biol. 2006;356:274-9 pubmed..Amide chemical shift changes map the RNA-binding site to a shallow, basic patch at the junction of helix alpha5 and the loop connecting helices alpha1 and alpha2. ..
- Gribun A, Kimber M, Ching R, Sprangers R, Fiebig K, Houry W. The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation. J Biol Chem. 2005;280:16185-96 pubmed publisher..Mutation of several amino acid residues in this loop or the truncation of the loop impairs ClpXP and ClpAP complex formation and prevents the coupling between ClpX/ClpA and ClpP activities...
- Saridakis V, Christendat D, Thygesen A, Arrowsmith C, Edwards A, Pai E. Crystal structure of Methanobacterium thermoautotrophicum conserved protein MTH1020 reveals an NTN-hydrolase fold. Proteins. 2002;48:141-3 pubmed
- Garces R, Wu N, Gillon W, Pai E. Anabaena circadian clock proteins KaiA and KaiB reveal a potential common binding site to their partner KaiC. EMBO J. 2004;23:1688-98 pubmed..Notably, the functionally relevant residues Arg 69 of KaiA and Arg 23 of KaiB align well in space. The apparent structural similarities suggest that KaiA and KaiB may compete for a potential common binding site on KaiC. ..
- van den Elsen J, Kuntz D, Rose D. Structure of Golgi alpha-mannosidase II: a target for inhibition of growth and metastasis of cancer cells. EMBO J. 2001;20:3008-17 pubmed..The enzyme-inhibitor interactions observed provide insight into the catalytic mechanism, opening the door to the design of novel inhibitors of alpha-mannosidase II. ..
- Davis T, Walker J, Loppnau P, Butler Cole C, Allali Hassani A, Dhe Paganon S. Autoregulation by the juxtamembrane region of the human ephrin receptor tyrosine kinase A3 (EphA3). Structure. 2008;16:873-84 pubmed publisher..This highly conserved set of residues likely delineates a molecular recognition pathway for most of the Eph RTKs, helping to characterize the dynamic nature of these physiologically important enzymes. ..
- Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, et al. Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli. J Mol Biol. 2007;374:1091-103 pubmed..Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases. ..
- Avvakumov G, Walker J, Xue S, Li Y, Duan S, Bronner C, et al. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1. Nature. 2008;455:822-5 pubmed publisher..The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG. ..
- Ceccarelli D, Blasutig I, Goudreault M, Li Z, Ruston J, Pawson T, et al. Non-canonical interaction of phosphoinositides with pleckstrin homology domains of Tiam1 and ArhGAP9. J Biol Chem. 2007;282:13864-74 pubmed..We posit that the diversity in PI interaction modes displayed by PH domains contributes to their versatility of use in biological systems. ..
- Sun W, Singh S, Zhang R, Turnbull J, Christendat D. Crystal structure of prephenate dehydrogenase from Aquifex aeolicus. Insights into the catalytic mechanism. J Biol Chem. 2006;281:12919-28 pubmed..This observation suggests that the two functional domains of chorismate mutase-prephenate dehydrogenase are interdependent and explains why these domains cannot be separated. ..
- Chan M, Karasawa S, Mizuno H, Bosanac I, Ho D, Prive G, et al. Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone Cnidopus japonicus. J Biol Chem. 2006;281:37813-9 pubmed..We conclude that the dynamics and structure of the chromophore are both essential for the optical appearance of these color proteins. ..
- Schuetz A, Allali Hassani A, Martin F, Loppnau P, Vedadi M, Bochkarev A, et al. Structural basis for molecular recognition and presentation of histone H3 by WDR5. EMBO J. 2006;25:4245-52 pubmed..We propose a mechanism for the involvement of WDR5 in binding and presenting histone H3K4 for further methylation as a component of MLL complexes. ..
- Pak J, Arnoux P, Zhou S, Sivarajah P, Satkunarajah M, Xing X, et al. X-ray crystal structure of leukocyte type core 2 beta1,6-N-acetylglucosaminyltransferase. Evidence for a convergence of metal ion-independent glycosyltransferase mechanism. J Biol Chem. 2006;281:26693-701 pubmed
- Xu C, Bian C, Yang W, Galka M, Ouyang H, Chen C, et al. Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proc Natl Acad Sci U S A. 2010;107:19266-71 pubmed publisher..In addition to determining the molecular basis of EED-methyllysine recognition, our work provides the biochemical characterization of how the activity of a histone methyltransferase is oppositely regulated by two histone marks. ..
- Sampaleanu L, Vall e F, Slingsby C, Howell P. Structural studies of duck delta 1 and delta 2 crystallin suggest conformational changes occur during catalysis. Biochemistry. 2001;40:2732-42 pubmed..The duck delta1 crystallin structure suggests that Ser 281, a residue strictly conserved in all members of the superfamily, could be the catalytic acid in the delta2 crystallin/ASL enzymatic mechanism...
- Lee J, Settembre E, Cornell K, Riscoe M, Sufrin J, Ealick S, et al. Structural comparison of MTA phosphorylase and MTA/AdoHcy nucleosidase explains substrate preferences and identifies regions exploitable for inhibitor design. Biochemistry. 2004;43:5159-69 pubmed..Sequence alignments of Escherichia coli MTAN, human MTAP, and plant MTA nucleosidases also reveal potential structural changes to the 5'-alkylthio binding site that account for the substrate preference of plant MTA nucleosidases. ..
- Lobsanov Y, Romero P, Sleno B, Yu B, Yip P, Herscovics A, et al. Structure of Kre2p/Mnt1p: a yeast alpha1,2-mannosyltransferase involved in mannoprotein biosynthesis. J Biol Chem. 2004;279:17921-31 pubmed..The importance of Tyr(220) in both mechanisms is highlighted by a 3000-fold reduction in k(cat) in the Y220F mutant. ..
- Bochkarev A, Bochkareva E, Frappier L, Edwards A. The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding. EMBO J. 1999;18:4498-504 pubmed..The structure also suggests a mechanism for RPA trimer formation. ..
- Mittag T, Marsh J, Grishaev A, Orlicky S, Lin H, Sicheri F, et al. Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure. 2010;18:494-506 pubmed publisher..These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. ..
- Wernimont A, Artz J, Finerty P, Lin Y, Amani M, Allali Hassani A, et al. Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium. Nat Struct Mol Biol. 2010;17:596-601 pubmed publisher..This large conformational change constitutes a distinct mechanism in calcium signal-transduction pathways...
- Payandeh J, Fujihashi M, Gillon W, Pai E. The crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase reveals an ancient fold for an ancient enzyme. J Biol Chem. 2006;281:6070-8 pubmed publisher..Sequence and structural comparisons lead us to postulate an early evolutionary history for AfGGGPS, which may highlight its role in the emergence of Archaea...
- Sim L, Quezada Calvillo R, Sterchi E, Nichols B, Rose D. Human intestinal maltase-glucoamylase: crystal structure of the N-terminal catalytic subunit and basis of inhibition and substrate specificity. J Mol Biol. 2008;375:782-92 pubmed..The results provide a structural basis for the complementary roles of these glycosyl hydrolase family 31 subunits in the bioprocessing of complex starch structures into glucose. ..
- Wu H, Horton J, Battaile K, Allali Hassani A, Martin F, Zeng H, et al. Structural basis of allele variation of human thiopurine-S-methyltransferase. Proteins. 2007;67:198-208 pubmed
- Gonzalez C, Proudfoot M, Brown G, Korniyenko Y, Mori H, Savchenko A, et al. Molecular basis of formaldehyde detoxification. Characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J Biol Chem. 2006;281:14514-22 pubmed..Thus, FrmB and YeiG are S-formylglutathione hydrolases with a Ser-His-Asp catalytic triad involved in the detoxification of formaldehyde in E. coli. ..
- Ahmad K, Melnick A, Lax S, Bouchard D, Liu J, Kiang C, et al. Mechanism of SMRT corepressor recruitment by the BCL6 BTB domain. Mol Cell. 2003;12:1551-64 pubmed..Two SMRT fragments bind symmetrically to the BCL6 BTB homodimer and, in combination with biochemical and in vivo data, the structure provides insight into the basis of transcriptional repression by this critical B cell lymphoma protein. ..
- Cho Y, Zunic V, Senboku H, Olsen M, Lautens M. Rhodium-catalyzed ring-opening reactions of N-boc-azabenzonorbornadienes with amine nucleophiles. J Am Chem Soc. 2006;128:6837-46 pubmed..2 eq to Rh) of the chiral ligand plays an important role to improve the enantioselectivity in the present asymmetric reaction...
- Notenboom V, Birsan C, Warren R, Withers S, Rose D. Exploring the cellulose/xylan specificity of the beta-1,4-glycanase cex from Cellulomonas fimi through crystallography and mutation. Biochemistry. 1998;37:4751-8 pubmed..Subsequent mutagenesis studies will address the role of entropic versus enthalpic contributions to binding by introducing side chains that might be more rigid in the unliganded enzyme...
- Yip C, Ottensmeyer P. Three-dimensional structural interactions of insulin and its receptor. J Biol Chem. 2003;278:27329-32 pubmed
- Isenman D, Leung E, Mackay J, Bagby S, van den Elsen J. Mutational analyses reveal that the staphylococcal immune evasion molecule Sbi and complement receptor 2 (CR2) share overlapping contact residues on C3d: implications for the controversy regarding the CR2/C3d cocrystal structure. J Immunol. 2010;184:1946-55 pubmed publisher..The results with CR2 confirm our earlier mapping studies and cast even further doubt on the physiologic relevance of the complex visualized in the C3d:CR2 cocrystal. ..
- Nagar B, Jones R, Diefenbach R, Isenman D, Rini J. X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2. Science. 1998;280:1277-81 pubmed..The structure supports a model whereby the transition of native C3 to its functionally active state involves the disruption of a complementary domain interface and provides insight into the basis for the interaction between C3d and CR2. ..
- Wu N, Gillon W, Pai E. Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography. Biochemistry. 2002;41:4002-11 pubmed..Consequently, orotidine 5'-monophosphate decarboxylases seem to require the presence of a negative charge at this position for catalysis as well as for correct and stable folding. ..
- Bochkareva E, Martynowski D, Seitova A, Bochkarev A. Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA. EMBO J. 2006;25:5961-9 pubmed..Our observations taken together with the known biochemical and structural features of the T-ag-origin interaction suggest a model for origin unwinding...
- Sheng Y, Saridakis V, Sarkari F, Duan S, Wu T, Arrowsmith C, et al. Molecular recognition of p53 and MDM2 by USP7/HAUSP. Nat Struct Mol Biol. 2006;13:285-91 pubmed..These results help to elucidate the mechanism of substrate recognition by USP7 and the regulation of the p53 pathway. ..
- Gorelik M, Lunin V, Skarina T, Savchenko A. Structural characterization of GntR/HutC family signaling domain. Protein Sci. 2006;15:1506-11 pubmed..The structural comparison of the C-PhnF and UbiC proteins allows us to propose that a similar site in the PhnF structure is adapted for effector binding. ..
- Mrkobrada S, Boucher L, Ceccarelli D, Tyers M, Sicheri F. Structural and functional analysis of Saccharomyces cerevisiae Mob1. J Mol Biol. 2006;362:430-40 pubmed..The N-terminal region of Mob1 thus contains structural elements that are functionally important. ..
- White A, Tull D, Johns K, Withers S, Rose D. Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase. Nat Struct Biol. 1996;3:149-54 pubmed..The active-site architecture of this covalent intermediate gives insights into both the classical double-displacement catalytic mechanism and the basis for the enzyme's specificity...
- Bosanac I, Alattia J, Mal T, Chan J, Talarico S, Tong F, et al. Structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with its ligand. Nature. 2002;420:696-700 pubmed..Putative Ca2+-binding sites are identified in two separate locations within the InsP3-binding core. ..
- Lunin V, Dobrovetsky E, Khutoreskaya G, Zhang R, Joachimiak A, Doyle D, et al. Crystal structure of the CorA Mg2+ transporter. Nature. 2006;440:833-7 pubmed..An apparent Mg2+ ion was bound between monomers at a conserved site in the cytoplasmic domain, suggesting a mechanism to link gating of the pore to the intracellular concentration of Mg2+. ..
- Sarkari F, La Delfa A, Arrowsmith C, Frappier L, Sheng Y, Saridakis V. Further insight into substrate recognition by USP7: structural and biochemical analysis of the HdmX and Hdm2 interactions with USP7. J Mol Biol. 2010;402:825-37 pubmed publisher..These results lead to a better understanding of the mechanism of substrate recognition by USP7-NTD. ..
- Sampaleanu L, Vallee F, Thompson G, Howell P. Three-dimensional structure of the argininosuccinate lyase frequently complementing allele Q286R. Biochemistry. 2001;40:15570-80 pubmed