当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus.

Crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus.

Abstract：

:The crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus KM1 has been solved by multiple isomorphous replacement. The enzyme is an alpha-amylase (family 13) with unique exo-amylolytic activity for glycosyltrehalosides. It cleaves the alpha-1,4 glycosidic bond adjacent to the trehalose moiety to release trehalose and maltooligo saccharide. Unlike most other family 13 glycosidases, the enzyme does not require Ca(2+) for activity, and it contains an N-terminal extension of approximately 100 amino acid residues that is homologous to N-terminal domains found in many glycosidases that recognize branched oligosaccharides. Crystallography revealed the enzyme to exist as a homodimer covalently linked by an intermolecular disulfide bond at residue C298. The existence of the intermolecular disulfide bond was confirmed by biochemical analysis and mutagenesis. The N-terminal extension forms an independent domain connected to the catalytic domain by an extended linker. The functionally essential Ca(2+) binding site found in the B domain of alpha-amylases and many other family 13 glycosidases was found to be replaced by hydrophobic packing interactions. The enzyme also contains a very unusual excursion in the (beta/alpha)(8) barrel structure of the catalytic domain. This excursion originates from the bottom of the (beta/alpha)(8) barrel between helix 6 and strand 7, but folds upward in a distorted alpha-hairpin structure to form a part of the substrate binding cleft wall that is possibly critical for the enzyme's unique substrate selectivity. Participation of an alpha-beta loop in the formation of the substrate binding cleft is a novel feature that is not observed in other known (beta/alpha)(8) enzymes.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Feese MD,Kato Y,Tamada T,Kato M,Komeda T,Miura Y,Hirose M,Hondo K,Kobayashi K,Kuroki R

doi

10.1006/jmbi.2000.3977

keywords:

subject

Has Abstract

pub_date

2000-08-11 00:00:00

pages

451-64

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)93977-9

journal_volume

301

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes.

    abstract：:Nonstandard nucleotide triphosphate pyrophosphatase (NTPase) can efficiently hydrolyze nonstandard purine nucleotides in the presence of divalent cations. The crystal structures of the NTPase from Pyrococcus horikoshii OT3 (PhNTPase) have been determined in two unliganded forms and in three liganded forms with inosine...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.11.018

    authors： Lokanath NK,Pampa KJ,Takio K,Kunishima N

    更新日期：2008-01-25 00:00:00

  • A stable alpha-helix-rich intermediate is formed by a single mutation of the beta-sheet protein, src SH3, at pH 3.

    abstract：:Recently, we have found a transient intermediate on the folding pathway of src SH3. Intending to investigate the structure of the transient intermediate, we tested a mutant of src SH3, named A45G, using circular dichroism, fluorescence and X-ray solution scattering, and incidentally found that it forms a stable alpha-...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.07.001

    authors： Li J,Matsumura Y,Shinjo M,Kojima M,Kihara H

    更新日期：2007-09-21 00:00:00

  • The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function.

    abstract：:Fatty acid biosynthesis is essential for the survival of Mycobacterium tuberculosis and acetyl-coenzyme A (acetyl-CoA) is an essential precursor in this pathway. We have determined the 3-D crystal structure of M. tuberculosis citrate lyase beta-subunit (CitE), which as annotated should cleave protein bound citryl-CoA ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.09.086

    authors： Goulding CW,Bowers PM,Segelke B,Lekin T,Kim CY,Terwilliger TC,Eisenberg D

    更新日期：2007-01-12 00:00:00

  • RNA editing in Drosophila 4f-rnp gene nuclear transcripts by multiple A-to-G conversions.

    abstract：:Pre-mRNA editing results in production of transcripts having nucleotide sequences differing from that of the DNA template. We describe the first example of RNA editing in the fruitfly Drosophila melanogaster. This editing occurs in an alternatively spliced adult head transcript arising from the single-copy nuclear 4f-...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0365

    authors： Petschek JP,Mermer MJ,Scheckelhoff MR,Simone AA,Vaughn JC

    更新日期：1996-06-28 00:00:00

  • Intramolecular DNA triplexes, bent DNA and DNA unwinding elements in the initiation region of an amplified dihydrofolate reductase replicon.

    abstract：:The nucleotide sequence of 6.2 kb (1 kb = 10(3) base-pairs) of DNA that encompasses the earliest replicating portion of the amplified dihydrofolate reductase domains of CHOC 400 cells has been determined. Origin region DNA contains two AluI family repeats, a novel repetitive element (termed ORR-1), a TGGGT-rich region...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(90)90008-A

    authors： Caddle MS,Lussier RH,Heintz NH

    更新日期：1990-01-05 00:00:00

  • Characterization of preferred deoxyribonuclease I cleavage sites.

    abstract：:The preferred DNase I cleavage sites within the 160 bp tyrT DNA fragment were identified by studying the initial rate of cleavage of individual bonds. The results show that there is no correlation between the rate of cleavage and the identity of the dinucleotide sequence that is cleaved. Examination of the sequences s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1152

    authors： Herrera JE,Chaires JB

    更新日期：1994-02-18 00:00:00

  • The role of backbone motions in ligand binding to the c-Src SH3 domain.

    abstract：:The Src homology 3 (SH3) domain of pp60(c-src) (Src) plays dual roles in signal transduction, through stabilizing the repressed form of the Src kinase and through mediating the formation of activated signaling complexes. Transition of the Src SH3 domain between a variety of binding partners during progression through ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5083

    authors： Wang C,Pawley NH,Nicholson LK

    更新日期：2001-11-02 00:00:00

  • Canonical antigen-binding loop structures in immunoglobulins: more structures, more canonical classes?

    abstract：:Grafting the antigen-binding loops onto a human antibody scaffold is a widely used technique to humanise murine antibodies. The success of this approach depends largely on the observation that the antigen-binding loops adopt only a limited number of canonical structures. Identification of the correct canonical structu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3839

    authors： Decanniere K,Muyldermans S,Wyns L

    更新日期：2000-06-30 00:00:00

  • Tests of the single-hit DNA damage model.

    abstract：:The algebra of target theory for damage by radiation was laid out by Atwood and Norman in 1949. Their equations provide a widely embraced framework for distinguishing single-hit and multi-hit mechanisms of damage. The present work asks whether in vitro damage to DNA duplexes by different agents affects amplification b...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.07.012

    authors： Spangler R,Goddard NL,Spangler DN,Thaler DS

    更新日期：2009-09-18 00:00:00

  • Delineation of the complement receptor type 2-C3d complex by site-directed mutagenesis and molecular docking.

    abstract：:The interactions between the complement receptor type 2 (CR2) and the C3 complement fragments C3d, C3dg, and iC3b are essential for the initiation of a normal immune response. A crystal-derived structure of the two N-terminal short consensus repeat (SCR1-2) domains of CR2 in complex with C3d has previously been elucid...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.10.005

    authors： Shaw CD,Storek MJ,Young KA,Kovacs JM,Thurman JM,Holers VM,Hannan JP

    更新日期：2010-12-10 00:00:00

  • DNA polymerase X from African swine fever virus: quantitative analysis of the enzyme-ssDNA interactions and the functional structure of the complex.

    abstract：:Interactions of polymerase X from African swine fever virus with single-stranded DNA (ssDNA) have been studied, using quantitative fluorescence titration and analytical ultracentrifugation techniques. Experiments were performed with a fluorescent etheno-derivative of ssDNA oligomers. Studies of unmodified ssDNA oligom...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.10.061

    authors： Jezewska MJ,Marcinowicz A,Lucius AL,Bujalowski W

    更新日期：2006-02-10 00:00:00

  • Yeast a1 and alpha 2 homeodomain proteins form a DNA-binding activity with properties distinct from those of either protein.

    abstract：:The yeast a1 and alpha 2 proteins are examples of homeodomain proteins that display cell-type-specific expression. They are co-expressed in only one type of cell, the a/alpha cell, where they repress the expression of a group of target genes. Using purified proteins, we demonstrate that a1 and alpha 2 form a highly sp...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1517

    authors： Goutte C,Johnson AD

    更新日期：1993-10-05 00:00:00

  • Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy.

    abstract：:Scaffold or matrix-attachment regions (S/MARs) are thought to be involved in the organization of eukaryotic chromosomes and in the regulation of several DNA functions. Their characteristics are conserved between plants and humans, and a variety of biological activities have been associated with them. The identificatio...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.11.073

    authors： Bode J,Winkelmann S,Götze S,Spiker S,Tsutsui K,Bi C,A K P,Benham C

    更新日期：2006-04-28 00:00:00

  • Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I.

    abstract：:The structure of the yeast DNA-dependent RNA polymerase I (RNA Pol I), prepared by cryo-negative staining, was studied by electron microscopy. A structural model of the enzyme at a resolution of 1.8 nm was determined from the analysis of isolated molecules and showed an excellent fit with the atomic structure of the R...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00510-2

    authors： De Carlo S,Carles C,Riva M,Schultz P

    更新日期：2003-06-20 00:00:00

  • Confidence limits for homology in protein or gene sequences. The c-myc oncogene and adenovirus E1a protein.

    abstract：:We describe new tests, of general application, for deciding whether two proteins or DNA sequences are significantly homologous, in cases where the relationship is neither evidently true nor evidently false. Ralston and Bishop's comparison of the c-myc oncogene with the adenovirus E1a protein is discussed as an example...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90181-0

    authors： McLachlan AD,Boswell DR

    更新日期：1985-09-05 00:00:00

  • Evidence that the KH RNA-binding domains influence the action of the E. coli NusA protein.

    abstract：:The NusA transcription elongation protein, which binds RNA, contains sequences corresponding to the S1 and KH classes of identified RNA binding domains. An essential function in E. coli, NusA is also one of the host factors required for action of the N transcription antitermination protein of lambda. Tandem KH domains...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00238-3

    authors： Zhou Y,Mah TF,Greenblatt J,Friedman DI

    更新日期：2002-05-17 00:00:00

  • Bcl-2 and porin follow different pathways of TOM-dependent insertion into the mitochondrial outer membrane.

    abstract：:The bcl-2 gene encodes a 26kDa protein which functions as a central regulator of apoptosis. Here we investigated the pathway of Bcl-2alpha into the mitochondrial outer membrane using the yeast Saccharomyces cerevisiae as a model organism. We found that interactions of Bcl-2alpha with the mitochondrial import receptor ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00995-6

    authors： Motz C,Martin H,Krimmer T,Rassow J

    更新日期：2002-11-01 00:00:00

  • Mechanism of strand cleavage and exchange in the Cre-lox site-specific recombination system.

    abstract：:The bacteriophage P1 recombinase Cre mediates site-specific recombination between loxP sites. The loxP site consists of two 13 base-pair inverted repeats separated by an eight base-pair spacer region. When DNA containing the loxP site is incubated with Cre, specific cleavages occur within the spacer region, creating a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90224-4

    authors： Hoess RH,Abremski K

    更新日期：1985-02-05 00:00:00

  • Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches.

    abstract：:The Bacillus subtilis extracytoplasmic function (ECF) sigma factor sigma(W) controls a large regulon that is strongly induced by alkali shock. To define the physiological role of sigma(W) we have sought to identify the complete set of genes under sigma(W) control. Previously, we described a promoter consensus search p...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5372

    authors： Cao M,Kobel PA,Morshedi MM,Wu MF,Paddon C,Helmann JD

    更新日期：2002-02-22 00:00:00

  • Sequence-dependent DNA structure: tetranucleotide conformational maps.

    abstract：:A database of X-ray crystal structures of double helical DNA oligomers has been used to analyse the role of the sugar-phosphate backbone in coupling the conformational properties of neighbouring dinucleotide steps. The base step parameters which are most strongly coupled to the backbone degrees of freedom are slide an...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3237

    authors： Packer MJ,Dauncey MP,Hunter CA

    更新日期：2000-01-07 00:00:00

  • Kinking of RNA helices by bulged bases, and the structure of the human immunodeficiency virus transactivator response element.

    abstract：:We have used gel electrophoresis to show that the pyrimidine bulge of the HIV-1 TAR sequence causes a local bending of the helical axis. The TAR bulge caused a retardation in electrophoretic mobility in polyacrylamide gels. When this was placed adjacent to an additional bulged sequence in a linear RNA fragment, the mo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90947-i

    authors： Riordan FA,Bhattacharyya A,McAteer S,Lilley DM

    更新日期：1992-07-20 00:00:00

  • Effect of Mg(2+) and Na(+) on the nucleic acid chaperone activity of HIV-1 nucleocapsid protein: implications for reverse transcription.

    abstract：:The human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) is an essential protein for retroviral replication. Among its numerous functions, NC is a nucleic acid (NA) chaperone protein that catalyzes NA rearrangements leading to the formation of thermodynamically more stable conformations. In vitro, NC ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.12.073

    authors： Vo MN,Barany G,Rouzina I,Musier-Forsyth K

    更新日期：2009-02-27 00:00:00

  • Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis.

    abstract：:A normal mode and energy minimization of ras p21 is used to determine the flexibility of the protein and the origin of the conformational differences between GTP and GDP-bound forms. To preserve the integrity of the structures, a hydration shell of water molecules was included as part of the system. Certain low-freque...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1313

    authors： Ma J,Karplus M

    更新日期：1997-11-21 00:00:00

  • Conformational flexibility and polymerization of vesicular stomatitis virus matrix protein.

    abstract：:The matrix protein of vesicular stomatitis virus (VSV) plays a pivotal role in viral assembly. We previously demonstrated the ability of M protein to self-associate at low salt concentrations. Now, we show the ability of M protein to polymerize in the presence of ZnCl2 in a nucleation-dependent manner. Analysis of kin...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1439

    authors： Gaudin Y,Sturgis J,Doumith M,Barge A,Robert B,Ruigrok RW

    更新日期：1997-12-19 00:00:00

  • Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling.

    abstract：:Archaeal dual-guide box C/D small nucleolar RNA-like RNAs (sRNAs) bind three core proteins in sequential order at both terminal box C/D and internal C'/D' motifs to assemble two ribonuclear protein (RNP) complexes active in guiding nucleotide methylation. Experiments have investigated the process of box C/D sRNP assem...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.07.091

    authors： Gagnon KT,Zhang X,Agris PF,Maxwell ES

    更新日期：2006-10-06 00:00:00

  • In vivo and in vitro studies of TrpR-DNA interactions.

    abstract：:The binding of tryptophan repressor (TrpR) to its operators was examined quantitatively using in vitro and in vivo methods. DNA sequence requirements for 1:1 and tandem 2:1 (TrpR:DNA) binding in various sequence contexts were studied. The results indicate that the optimal half-site sequence for recognition by one heli...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0232

    authors： Yang J,Gunasekera A,Lavoie TA,Jin L,Lewis DE,Carey J

    更新日期：1996-04-26 00:00:00

  • Crystal structure of an active form of human MMP-1.

    abstract：:The extracellular matrix is a dynamic environment that constantly undergoes remodelling and degradation during vital physiological processes such as angiogenesis, wound healing, and development. Unbalanced extracellular matrix breakdown is associated with many diseases such as arthritis, cancer and fibrosis. Interstit...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.06.079

    authors： Iyer S,Visse R,Nagase H,Acharya KR

    更新日期：2006-09-08 00:00:00

  • Complete assignment of the 1H nuclear magnetic resonance spectrum of French bean plastocyanin. Sequential resonance assignments, secondary structure and global fold.

    abstract：:Sequence-specific proton nuclear magnetic resonance (n.m.r.) assignments for all 99 amino acid residues of French bean Cu(I) plastocyanin are described. The assignments were made using standard sequential assignment procedures and were greatly facilitated by the availability of complete spin system assignments. The ch...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90291-4

    authors： Chazin WJ,Wright PE

    更新日期：1988-08-05 00:00:00

  • Repressor assembly at trp binding sites is dependent on the identity of the intervening dinucleotide between the binding half sites.

    abstract：:The interaction of trp repressor with its DNA targets is unusual in that specific recognition in this system does not rely exclusively on direct hydrogen bonds to the DNA bases that are crucial for sequence-specific recognition. It has been suggested that trp operators are mainly recognized by water-mediated interacti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0826

    authors： Bareket-Samish A,Cohen I,Haran TE

    更新日期：1997-03-21 00:00:00

  • Peroxisome proliferator-activated receptor alpha controls hepatic heme biosynthesis through ALAS1.

    abstract：:Heme is an essential prosthetic group of proteins involved in oxygen transport, energy metabolism and nitric oxide production. ALAS1 (5-aminolevulinate synthase) is the rate-limiting enzyme in heme synthesis in the liver and is highly regulated to adapt to the metabolic demand of the hepatocyte. In the present study, ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,收录出版

    doi：10.1016/j.jmb.2009.03.024

    authors： Degenhardt T,Väisänen S,Rakhshandehroo M,Kersten S,Carlberg C

    更新日期：2009-05-01 00:00:00