Beta-propeller crystal structure of Psathyrella velutina lectin: an integrin-like fungal protein interacting with monosaccharides and calcium.

Abstract:

:The lectin from the mushroom Psathyrella velutina recognises specifically N-acetylglucosamine and N-acetylneuraminic acid containing glycans. The crystal structure of the 401 amino acid residue lectin shows that it adopts a very regular seven-bladed beta-propeller fold with the N-terminal region tucked into the central cavity around the pseudo 7-fold axis. In the complex with N-acetylglucosamine, six monosaccharides are bound in pockets located between two consecutive propeller blades. Due to the repeats shown by the sequence the binding sites are very similar. Five hydrogen bonds between the protein and the sugar hydroxyl and N-acetyl groups stabilize the complex, together with the hydrophobic interactions with a conserved tyrosine and histidine. The complex with N-acetylneuraminic acid shows molecular mimicry with the same hydrogen bond network, but with different orientations of the carbohydrate ring in the binding site. The beta-hairpin loops connecting the two inner beta-strands of each blade are metal binding sites and two to three calcium ions were located in the structure. The multispecificity and high multivalency of this mushroom lectin, combined with its similarity to the extracellular domain of an important class of cell adhesion molecules, integrins, are another example of the outstanding success of beta-propeller structures as molecular binding machines in nature.

journal_name

J Mol Biol

authors

Cioci G,Mitchell EP,Chazalet V,Debray H,Oscarson S,Lahmann M,Gautier C,Breton C,Perez S,Imberty A

doi

10.1016/j.jmb.2006.01.066

keywords:

subject

Has Abstract

pub_date

2006-04-14 00:00:00

pages

1575-91

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(06)00107-0

journal_volume

357

pub_type

杂志文章
  • Prediction of transcription terminators in bacterial genomes.

    abstract::This study describes an algorithm that finds rho-independent transcription terminators in bacterial genomes and evaluates the accuracy of its predictions. The algorithm identifies terminators by searching for a common mRNA motif: a hairpin structure followed by a short uracil-rich region. For each terminator, an energ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3836

    authors: Ermolaeva MD,Khalak HG,White O,Smith HO,Salzberg SL

    更新日期:2000-08-04 00:00:00

  • Crystallization and preliminary diffraction studies of Erythrina trypsin inhibitor.

    abstract::Crystals of an inhibitor of trypsin and tissue plasminogen activator from seeds of the legume Erythrina caffra have been obtained by vapour diffusion. The crystals belong to the hexagonal space group P6(1)22 (or its enantiomorph P6(5)22) with cell parameters 73.4 A and 143.0 A. There is one molecule in the asymmetric ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90306-9

    authors: Onesti S,Lloyd LF,Maeder D,Mistry A,Brick P

    更新日期:1989-11-05 00:00:00

  • Weak and strong states of kinesin and ncd.

    abstract::Kinesin superfamily molecular motors step along microtubules (MTs) via a cycle of conformational changes which is coupled to ATP turnover. To probe the coupling mechanism, we titrated the effects of various nucleotides on MT binding by two superfamily members; MT plus-end-directed kinesin and MT minus-end-directed non...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0147

    authors: Crevel IM,Lockhart A,Cross RA

    更新日期:1996-03-22 00:00:00

  • The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.

    abstract::Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. These combine high-re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.11.032

    authors: van Zundert GC,Trellet M,Schaarschmidt J,Kurkcuoglu Z,David M,Verlato M,Rosato A,Bonvin AM

    更新日期:2017-02-03 00:00:00

  • Detection of transmembrane linkages between immunoglobulin or complement receptors and the neutrophil's cortical microfilaments by resonance energy transfer microscopy.

    abstract::By exploiting the 1/r4 (where r is the separation distance between fluorochromes) dependence of energy transfer between parallel lamellae, we have observed transmembrane energy transfer between membrane receptors and cortical microfilaments. Receptors were labeled with donor- or acceptor-conjugated Fab fragments, wher...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90709-f

    authors: Zhou MJ,Todd RF 3rd,Petty HR

    更新日期:1991-03-20 00:00:00

  • Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase.

    abstract::The structure of the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase in complex with cognate DNA was determined at 1.89 A resolution in the presence of S-adenosyl-L-homocysteine. DNA recognition and the dynamics of base-flipping were studied by site-directed mutagenesis, DNA methylation kinetics and fluorescen...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.02.028

    authors: Horton JR,Liebert K,Bekes M,Jeltsch A,Cheng X

    更新日期:2006-04-28 00:00:00

  • Nucleation and polymerization of sickle hemoglobin with Leu beta 88 substituted by Ala.

    abstract::We have measured the solubility, and the rates of homogeneous and heterogeneous nucleation on sickle hemoglobin (HbS beta 6 Glu-->Val) additionally modified by site-directed mutagenesis to possess Ala rather than Leu at beta 88, which forms part of the receptor site for beta 6 Val in the sickle polymer. The solubility...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0749

    authors: Cao Z,Liao D,Mirchev R,Martin de Llano JJ,Himanen JP,Manning JM,Ferrone FA

    更新日期:1997-02-07 00:00:00

  • Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli.

    abstract::Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+ antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.10.028

    authors: Kedrov A,Janovjak H,Ziegler C,Kuhlbrandt W,Muller DJ

    更新日期:2006-01-06 00:00:00

  • Construction of a microphage variant of filamentous bacteriophage.

    abstract::The intergenic region in the genome of the Ff class of filamentous phage (comprising strains fl, fd and M13) genome constitutes 8% of the viral genome, and has essential functions in DNA replication and phage morphogenesis. The functional domains of this region may be inserted into separate sites of a plasmid to funct...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90858-h

    authors: Specthrie L,Bullitt E,Horiuchi K,Model P,Russel M,Makowski L

    更新日期:1992-12-05 00:00:00

  • A thiol labelling competition experiment as a probe for sidechain packing in the kinetic folding intermediate of N-PGK.

    abstract::Protein folding is directed by the sequence of sidechains along the polypeptide backbone, but despite this the developement of sidechain interactions during folding is not well understood. Here, the thiol-active reagent, dithio-nitrobenzoic acid (DTNB), is used to probe the exposure of the cysteine sidechain thiols in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.09.014

    authors: Cliff MJ,Alizadeh T,Jelinska C,Craven CJ,Staniforth RA,Waltho JP

    更新日期:2006-12-08 00:00:00

  • Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study.

    abstract::We have applied a search strategy for determining the optimal packing of protein secondary structure elements to the rotational positioning of the seven transmembrane helices of bacteriorhodopsin. The search is based on the assumption that the relative orientations of the helices within the bundle are conditioned prin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(94)90015-9

    authors: Tuffery P,Etchebest C,Popot JL,Lavery R

    更新日期:1994-03-04 00:00:00

  • The crystal structure of Thermotoga maritima maltosyltransferase and its implications for the molecular basis of the novel transfer specificity.

    abstract::Maltosyltransferase (MTase) from the hyperthermophile Thermotoga maritima represents a novel maltodextrin glycosyltransferase acting on starch and malto-oligosaccharides. It catalyzes the transfer of maltosyl units from alpha-1,4-linked glucans or malto-oligosaccharides to other alpha-1,4-linked glucans, malto-oligosa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4944

    authors: Roujeinikova A,Raasch C,Burke J,Baker PJ,Liebl W,Rice DW

    更新日期:2001-09-07 00:00:00

  • The Roles of Actin-Binding Domains 1 and 2 in the Calcium-Dependent Regulation of Actin Filament Bundling by Human Plastins.

    abstract::The actin cytoskeleton is a complex network controlled by a vast array of intricately regulated actin-binding proteins. Human plastins (PLS1, PLS2, and PLS3) are evolutionary conserved proteins that non-covalently crosslink actin filaments into tight bundles. Through stabilization of such bundles, plastins contribute,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2017.06.021

    authors: Schwebach CL,Agrawal R,Lindert S,Kudryashova E,Kudryashov DS

    更新日期:2017-08-04 00:00:00

  • Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution.

    abstract::The factor for inversion stimulation (FIS) binds as a homodimeric molecule to a loose 15 nucleotide consensus sequence in DNA. It stimulates DNA-related processes, such as DNA inversion and excision, it activates transcription of tRNA and rRNA genes and it regulates its own synthesis. FIS crystallizes as a homodimer, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90134-6

    authors: Kostrewa D,Granzin J,Stock D,Choe HW,Labahn J,Saenger W

    更新日期:1992-07-05 00:00:00

  • Packaging of a unit-length viral genome: the role of nucleotides and the gpD decoration protein in stable nucleocapsid assembly in bacteriophage lambda.

    abstract::The developmental pathways for a variety of eukaryotic and prokaryotic double-stranded DNA viruses include packaging of viral DNA into a preformed procapsid structure, catalyzed by terminase enzymes and fueled by ATP hydrolysis. In most instances, a capsid expansion process accompanies DNA packaging, which significant...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.08.063

    authors: Yang Q,Maluf NK,Catalano CE

    更新日期:2008-11-28 00:00:00

  • X-ray analysis of the eye lens protein gamma-II crystallin at 1.9 A resolution.

    abstract::We report the X-ray structure analysis and refinement at 1.9 A resolution of calf gamma-II crystallin, a lens-specific protein. The sequence of Croft (1972) has been modified to give a polypeptide chain of 174 residues (cf. 165). The protein has a symmetrical, hierarchical structure of two globular domains each compri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80232-0

    authors: Wistow G,Turnell B,Summers L,Slingsby C,Moss D,Miller L,Lindley P,Blundell T

    更新日期:1983-10-15 00:00:00

  • An unusual conformation of NAD+ bound to sorbitol dehydrogenase? A time-dependent transferred nuclear Overhauser effect study.

    abstract::The conformation of NAD+ in the sheep liver sorbitol dehydrogenase-NAD+ binary complex has been investigated using time-dependent proton-proton transferred nuclear Overhauser enhancement measurements to determine interproton distance ratios and distances between bound NAD+ protons. The conformation about both the aden...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(84)80023-6

    authors: Gronenborn AM,Clore GM,Jeffery J

    更新日期:1984-02-05 00:00:00

  • The regions of the sequence most exposed to the solvent within the amyloidogenic state of a protein initiate the aggregation process.

    abstract::Formation of misfolded aggregates is an essential part of what proteins can do. The process of protein aggregation is central to many human diseases and any aggregating event needs to be prevented within a cell and in protein design. In order to aggregate, a protein needs to unfold its native state, at least partially...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.10.082

    authors: Monti M,Garolla di Bard BL,Calloni G,Chiti F,Amoresano A,Ramponi G,Pucci P

    更新日期:2004-02-06 00:00:00

  • Contribution of opening and bending dynamics to specific recognition of DNA damage.

    abstract::Guanine-uracil (G.U) wobble base-pairs are a detrimental lesion in DNA. Previous investigations have shown that such wobble base-pairs are more prone to base-opening than the normal G.C base-pairs. To investigate the sequence-dependence of base-pair opening we have performed 5ns molecular dynamics simulations on G.U w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00598-9

    authors: Seibert E,Ross JB,Osman R

    更新日期:2003-07-18 00:00:00

  • 3D gene of foot-and-mouth disease virus. Conservation by convergence of average sequences.

    abstract::The nucleotide sequence of the 3D (polymerase) gene of eight epidemiologically related isolates of foot-and-mouth disease virus of serotype C1 is reported. The genetic heterogeneity of 3D RNA is compared with that of the VP1-coding RNA of the same viruses. Regression lines of substitutions per nucleotide that distingu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90367-1

    authors: Villaverde A,Martínez-Salas E,Domingo E

    更新日期:1988-12-05 00:00:00

  • Time to be versatile: regulation of the replication timing program in budding yeast.

    abstract::Eukaryotic replication origins are activated at different times during the S phase of the cell cycle, following a temporal program that is stably transmitted to daughter cells. Although the mechanisms that control initiation at the level of individual origins are now well understood, much less is known on how cells co...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2013.09.020

    authors: Yoshida K,Poveda A,Pasero P

    更新日期:2013-11-29 00:00:00

  • Protein unfolding, and the "tuning in" of reversible intermediate states, in protic ionic liquid media.

    abstract::Protic ionic liquids (PILs) are currently being shown to be as interesting and valuable to chemical manipulations as the well-known aprotic ionic liquids (APIL). PILs have the additional advantage that the proton activity (PA) can be adjusted by the choice of Bronsted base and Bronsted acid used in their formation. In...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.02.050

    authors: Byrne N,Angell CA

    更新日期:2008-05-02 00:00:00

  • New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy.

    abstract::In the past several decades solution NMR spectroscopy has emerged as a powerful technique for the study of the structure and dynamics of proteins, providing detailed insights into biomolecular function. Herein, I provide a summary of two important areas of application, focusing on NMR studies of (i) supramolecular sys...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2015.11.028

    authors: Kay LE

    更新日期:2016-01-29 00:00:00

  • Structure and function of the hairpin ribozyme.

    abstract::The hairpin ribozyme belongs to the family of small catalytic RNAs that cleave RNA substrates in a reversible reaction that generates 2',3'-cyclic phosphate and 5'-hydroxyl termini. The hairpin catalytic motif was discovered in the negative strand of the tobacco ringspot virus satellite RNA, where hairpin ribozyme-med...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1006/jmbi.2000.3560

    authors: Fedor MJ

    更新日期:2000-03-24 00:00:00

  • Cloning and sequence analysis of the Escherichia coli 4.5 S RNA gene.

    abstract::The structure of the Escherichia coli gene coding for the metabolically stable 4.5 S RNA has been determined by cloning and DNA sequence analysis. Results from Southern hybridization assays carried out prior to cloning show the 4.5 S DNA to be limited to a single locus in the E. coli K12 genome. A 5.4 X 10(3) base DNA...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90236-5

    authors: Hsu LM,Zagorski J,Fournier MJ

    更新日期:1984-09-25 00:00:00

  • Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations.

    abstract::Mutational experiments show how changes in the hydrophobic cores of proteins affect their stabilities. Here, we estimate these effects computationally, using four-body likelihood potentials obtained by simplicial neighborhood analysis of protein packing (SNAPP). In this procedure, the volume of a known protein structu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4906

    authors: Carter CW Jr,LeFebvre BC,Cammer SA,Tropsha A,Edgell MH

    更新日期:2001-08-24 00:00:00

  • Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH.

    abstract::Foot-and-mouth disease virus (FMDV), a non-enveloped picornavirus, is sensitive to acidic conditions. At pH values below 7 the icosahedral virus capsid, formed from 60 copies of a protomer containing four polypeptides (VP1 to 4), dissociates into 12 pentamers, releasing the viral RNA. Evidence suggests that this acid ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1418

    authors: van Vlijmen HW,Curry S,Schaefer M,Karplus M

    更新日期:1998-01-16 00:00:00

  • Observing membrane protein diffusion at subnanometer resolution.

    abstract::Single sodium-driven rotors from a bacterial ATP synthase were embedded into a lipid membrane and observed in buffer solution at subnanometer resolution using atomic force microscopy (AFM). Time-lapse AFM topographs show the movement of single proteins within the membrane. Subsequent analysis of their individual traje...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00206-7

    authors: Müller DJ,Engel A,Matthey U,Meier T,Dimroth P,Suda K

    更新日期:2003-04-11 00:00:00

  • Generation, affinity maturation, and characterization of a human anti-human NKG2D monoclonal antibody with dual antagonistic and agonistic activity.

    abstract::In humans, NKG2D is an activating receptor on natural killer (NK) cells and a costimulatory receptor on certain T cells and plays a central role in mediating immune responses in autoimmune diseases, infectious diseases, and cancer. Monoclonal antibodies that antagonize or agonize immune responses mediated by human NKG...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.09.008

    authors: Kwong KY,Baskar S,Zhang H,Mackall CL,Rader C

    更新日期:2008-12-31 00:00:00

  • Characterization of two subunits of Arabidopsis 19S proteasome regulatory complex and its possible interaction with the COP9 complex.

    abstract::The nuclear localized, multi-subunit COP9 complex (or COP9 signalosome) is a key developmental modulator involved in repression of photomorphogenesis. In an effort to further define the molecular actions of the COP9 complex, a yeast two hybrid interactive screen was undertaken to identify proteins that could directly ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2315

    authors: Kwok SF,Staub JM,Deng XW

    更新日期:1999-01-08 00:00:00