Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution.

Abstract:

:The X-ray crystal structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) and alpha-amylase 2 (TVAII) have been determined at 1.6 A and 2.3 A resolution, respectively. The structures of TVAI and TVAII have been refined, R-factor of 0.182 (R(free)=0.206) and 0.179 (0.224), respectively, with good chemical geometries. Both TVAI and TVAII have four domains, N, A, B and C, and all very similar in structure. However, there are some differences in the structures between them. Domain N of TVAI interacts strongly with domains A and B, giving a spherical shape structure to the enzyme, while domain N of TVAII is isolated from the other domains, which leads to the formation of a dimer. TVAI has three bound Ca ions, whereas TVAII has only one. TVAI has eight extra loops compared to TVAII, while TVAII has two extra loops compared to TVAI. TVAI can hydrolyze substrates more efficiently than TVAII with a high molecular mass such as starch, while TVAII is much more active against cyclodextrins than TVAI and other alpha-amylases. A structural comparison of the active sites has clearly revealed this difference in substrate specificity.

journal_name

J Mol Biol

authors

Kamitori S,Abe A,Ohtaki A,Kaji A,Tonozuka T,Sakano Y

doi

10.1016/S0022-2836(02)00111-0

keywords:

subject

Has Abstract

pub_date

2002-04-26 00:00:00

pages

443-53

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(02)00111-0

journal_volume

318

pub_type

杂志文章
  • Bacterial Signaling to the Nervous System through Toxins and Metabolites.

    abstract::Mammalian hosts interface intimately with commensal and pathogenic bacteria. It is increasingly clear that molecular interactions between the nervous system and microbes contribute to health and disease. Both commensal and pathogenic bacteria are capable of producing molecules that act on neurons and affect essential ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2016.12.023

    authors: Yang NJ,Chiu IM

    更新日期:2017-03-10 00:00:00

  • The elastic I-band region of titin is assembled in a "modular" fashion by weakly interacting Ig-like domains.

    abstract::The vertebrate striated muscle protein titin is thought to play a critical rôle in myofibril assembly and passive tension. The recently determined complete primary structure of titin revealed a modular architecture that opens the way to a structural characterisation and the understanding of essential properties of thi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0050

    authors: Politou AS,Gautel M,Improta S,Vangelista L,Pastore A

    更新日期:1996-02-02 00:00:00

  • IS1-mediated tandem duplication of plasmid pBR322. Dependence on recA and on DNA polymerase I.

    abstract::Transposable-element-mediated fusion of the conjugal plasmid pOX38::Tn9 with pBR322 results in the appearance of cointegrates composed of a single copy of each plasmid, and cointegrates which carry a single copy of pOX38 but multiple tandem copies of pBR322. These plasmids are separated by directly repeated copies of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80249-6

    authors: Chandler M,Galas DJ

    更新日期:1983-03-25 00:00:00

  • Transcriptional regulation of mouse alphaB- and gammaF-crystallin genes in lens: opposite promoter-specific interactions between Pax6 and large Maf transcription factors.

    abstract::Mammalian alphaB-crystallin is highly expressed both in lens epithelium and lens fibers. In contrast, gammaF-crystallin is highly expressed in the lens fiber cells. Crystallin gene expression in lens is regulated at the level of transcription by a sparse number of specific DNA-binding transcription factors. Here, we r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.07.102

    authors: Yang Y,Chauhan BK,Cveklova K,Cvekl A

    更新日期:2004-11-19 00:00:00

  • Amino acid periodicities and their structural implications for the evolutionarily conservative central domain of some silkmoth chorion proteins.

    abstract::The central domain is an evolutionarily conservative region that is invariant in length in the A and Hc-A families of silkmoth chorion proteins. This domain shows strong sixfold periodicities for various amino acid residues, such as glycine and large non-polar residues. The periodicities and their phase relationships,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90132-9

    authors: Hamodrakas SJ,Etmektzoglou T,Kafatos FC

    更新日期:1985-12-05 00:00:00

  • Roles for glycosylation of cell surface receptors involved in cellular immune recognition.

    abstract::The majority of cell surface receptors involved in antigen recognition by T cells and in the orchestration of the subsequent cell signalling events are glycoproteins. The length of a typical N-linked sugar is comparable with that of an immunoglobulin domain (30 A). Thus, by virtue of their size alone, oligosaccharides...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1006/jmbi.1999.3104

    authors: Rudd PM,Wormald MR,Stanfield RL,Huang M,Mattsson N,Speir JA,DiGennaro JA,Fetrow JS,Dwek RA,Wilson IA

    更新日期:1999-10-22 00:00:00

  • Crystal structures of artocarpin, a Moraceae lectin with mannose specificity, and its complex with methyl-alpha-D-mannose: implications to the generation of carbohydrate specificity.

    abstract::The seeds of jack fruit (Artocarpus integrifolia) contain two tetrameric lectins, jacalin and artocarpin. Jacalin was the first lectin found to exhibit the beta-prism I fold, which is characteristic of the Moraceae plant lectin family. Jacalin contains two polypeptide chains produced by a post-translational proteolysi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5432

    authors: Pratap JV,Jeyaprakash AA,Rani PG,Sekar K,Surolia A,Vijayan M

    更新日期:2002-03-22 00:00:00

  • X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons.

    abstract::An open reading frame optimized for expression of 6,7-dimethyl-8-ribityl-lumazine synthase of the hyperthermophilic bacterium Aquifex aeolicus in Escherichia coli was synthesized and expressed in a recombinant E. coli strain to a level of around 15 %. The recombinant protein was purified by heat-treatment and gel-filt...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4435

    authors: Zhang X,Meining W,Fischer M,Bacher A,Ladenstein R

    更新日期:2001-03-09 00:00:00

  • Protein titration in the crystal state.

    abstract::Proteins are complex structures whose overall stability critically depends on a delicate balance of numerous interactions of similar strength, which are markedly influenced by their environment. Here, we present an analysis of the effect of pH on a protein structure in the crystalline state using RNase A as a model sy...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3093

    authors: Berisio R,Lamzin VS,Sica F,Wilson KS,Zagari A,Mazzarella L

    更新日期:1999-10-01 00:00:00

  • Invertebrate myosin filament: subfilament arrangement in the wall of tubular filaments of insect flight muscles.

    abstract::Transverse sections (100 to 140 nm thick) of the flight muscles of the fleshfly Phormia terrae-novae and the housefly Musca domestica were studied. The images of 56 tubular myosin filaments of the fleshfly and 62 filaments of the housefly were digitized and computer processed by rotational averaging. The rotational po...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90637-7

    authors: Beinbrech G,Ashton FT,Pepe FA

    更新日期:1988-06-05 00:00:00

  • Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain.

    abstract::The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divale...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.12.010

    authors: Welty R,Rau M,Pabit S,Dunstan MS,Conn GL,Pollack L,Hall KB

    更新日期:2020-02-14 00:00:00

  • Stability of a homo-dimeric Ca(2+)-binding member of the beta gamma-crystallin superfamily: DSC measurements on spherulin 3a from Physarum polycephalum.

    abstract::Spherulin 3a (S3a) from Physarum polycephalum represents the only known single-domain member of the superfamily of beta gamma eye-lens crystallins. It shares the typical two Greek-key motif and is stabilized by dimerization and Ca(2+)-binding. The temperature and denaturant-induced unfolding of S3a in the absence and ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3037

    authors: Kretschmar M,Jaenicke R

    更新日期:1999-09-03 00:00:00

  • Deletion analysis of the lambda tR1 termination region. Effect of sequences near the transcript release sites, and the minimum length of rho-dependent transcripts.

    abstract::In order to determine how much of the natural sequence is required for function of the lambda tR1 rho-dependent terminator, and to determine the minimum length required, we made two deletion series of a tR1 derivative that contains mostly foreign DNA, encoding C-rich RNA, substituted for the natural upstream sequences...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1229

    authors: Hart CM,Roberts JW

    更新日期:1994-04-01 00:00:00

  • Infrared dichroism of twisted beta-sheet barrels. The structure of E. coli outer membrane proteins.

    abstract::The infrared dichroic ratios of the amide bands from oriented beta-barrels yield an experimental value for the mean orientation, beta, of the beta-strands, relative to the barrel axis. For a barrel of n strands, this then gives the shear number, S, that characterizes the stagger of the beta-sheet. Combining values of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3557

    authors: Marsh D

    更新日期:2000-03-31 00:00:00

  • Hetero-assembly between all-L- and all-D-amino acid transmembrane domains: forces involved and implication for inactivation of membrane proteins.

    abstract::Protein-protein interactions within the membrane, partially or fully mediated by transmembrane (TM) domains, are involved in many vital cellular processes. Since the unique feature of the membrane environment enables protein-protein assembly that otherwise is not energetically favored in solution, the structural restr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.09.066

    authors: Sal-Man N,Gerber D,Shai Y

    更新日期:2004-11-26 00:00:00

  • Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts.

    abstract::Under usual laboratory conditions, lysis by bacteriophage lambda requires only the holin and endolysin genes, but not the Rz and Rz1 genes, of the lysis cassette. Defects in Rz or Rz1 block lysis only in the presence of high concentrations of divalent cations. The lambda Rz and Rz1 lysis genes are remarkable in that R...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.08.045

    authors: Summer EJ,Berry J,Tran TA,Niu L,Struck DK,Young R

    更新日期:2007-11-09 00:00:00

  • Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA.

    abstract::Methyltransferases from the m(1)A(58) tRNA methyltransferase (TrmI) family catalyze the S-adenosyl-l-methionine-dependent N(1)-methylation of tRNA adenosine 58. The crystal structure of Thermus thermophilus TrmI, in complex with S-adenosyl-l-homocysteine, was determined at 1.7 A resolution. This structure is closely r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.01.041

    authors: Barraud P,Golinelli-Pimpaneau B,Atmanene C,Sanglier S,Van Dorsselaer A,Droogmans L,Dardel F,Tisné C

    更新日期:2008-03-21 00:00:00

  • Analysis of protein main-chain solvation as a function of secondary structure.

    abstract::We have analysed the hydration of main-chain carbonyl and amide groups in 24 high-resolution well-refined protein structures as a function of the secondary structure in which these polar groups occur. We find that main-chain atoms in beta-sheets are as hydrated as those in alpha-helices, with most interactions involvi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)80080-e

    authors: Thanki N,Umrania Y,Thornton JM,Goodfellow JM

    更新日期:1991-09-20 00:00:00

  • Surface, subunit interfaces and interior of oligomeric proteins.

    abstract::The solvent-accessible surface area (As) of 23 oligomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. As is correlated with the protein molecular weight, and a power law predicts its value to within 5% on average. The accessible surface of the average olig...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90606-7

    authors: Janin J,Miller S,Chothia C

    更新日期:1988-11-05 00:00:00

  • Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination.

    abstract::Homologous recombination (HR) is an evolutionary-conserved mechanism involved in a subtle balance between genome stability and diversity. HR is a faithful DNA repair pathway and has been largely characterized in the context of double-strand break (DSB) repair. Recently, multiple functions for the HR machinery have bee...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2013.04.023

    authors: Carr AM,Lambert S

    更新日期:2013-11-29 00:00:00

  • Isolation and properties of transcribing ternary complexes of Escherichia coli RNA polymerase positioned at a single template base.

    abstract::We have studied the conditions needed for the formation of stable ternary complexes by Escherichia coli RNA polymerase using a procedure in which elongation by the majority of active enzyme molecules is halted at a specific template base. Stable complexes of this sort, containing RNA chains as short as 15 nucleotides,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90512-2

    authors: Levin JR,Krummel B,Chamberlin MJ

    更新日期:1987-07-05 00:00:00

  • Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases.

    abstract::The position of the tertiary Levitt pair between nucleotides 15 and 48 in the transfer RNA core region suggests a key role in stabilizing the joining of the two helical domains, and in maintaining the relative orientations of the D and variable loops. E. coli tRNA(Gln) possesses the canonical Pu15-Py48 trans pairing a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3749

    authors: Sherlin LD,Bullock TL,Newberry KJ,Lipman RS,Hou YM,Beijer B,Sproat BS,Perona JJ

    更新日期:2000-06-02 00:00:00

  • Promoter strength and structure dictate module composition in RNA polymerase III transcriptional activator elements.

    abstract::RNA polymerase III transcription of genes with external promoters only (e.g. U6 snRNA) or containing in addition an internal B box (selenocysteine tRNA(Sec)) is stimulated by upstream elements; a distal sequence element (DSE) for U6 or an activator element in the tRNA(Sec) gene. In contrast to the composite structure ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1588

    authors: Myslinski E,Schuster C,Krol A,Carbon P

    更新日期:1993-11-20 00:00:00

  • UHRF1 double tudor domain and the adjacent PHD finger act together to recognize K9me3-containing histone H3 tail.

    abstract::Human multi-domain-containing protein UHRF1 has recently been extensively characterized as a key epigenetic regulator for maintaining DNA methylation patterns. UHRF1 SRA domain preferentially binds to hemimethylated CpG sites, and double Tudor domain has been implicated in recognizing H3K9me3 mark, but the role of the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.11.012

    authors: Xie S,Jakoncic J,Qian C

    更新日期:2012-01-13 00:00:00

  • Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis.

    abstract::Although many putative heme transporters have been discovered, it has been challenging to prove that these proteins are directly involved with heme trafficking in vivo and to identify their heme binding domains. The prokaryotic pathways for cytochrome c biogenesis, Systems I and II, transport heme from inside the cell...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.01.022

    authors: Sutherland MC,Jarodsky JM,Ovchinnikov S,Baker D,Kranz RG

    更新日期:2018-04-13 00:00:00

  • The hypE gene completes the gene cluster for H2-oxidation in Azotobacter vinelandii.

    abstract::The nucleotide sequence was obtained for the hypE gene in the cluster of structural and accessory genes required for the assembly and functioning of the membrane-bound, dimeric, (NiFe)hydrogenase in Azotobacter vinelandii. The hypE gene encodes a polypeptide of 341 amino acid residues which is rich in alanine, glycine...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1149

    authors: Garg RP,Menon AL,Jacobs K,Robson RM,Robson RL

    更新日期:1994-02-11 00:00:00

  • Genetic interactions among the transmembrane segments of the G protein coupled receptor encoded by the yeast STE2 gene.

    abstract::G protein coupled receptors (GPCRs) are integral membrane proteins that mediate cellular responses to a wide variety of extracellular signals. However, the structural basis for activation of this class of receptors by ligand binding is not well understood. We report here the use of a systematic genetic protocol for id...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0816

    authors: Sommers CM,Dumont ME

    更新日期:1997-02-28 00:00:00

  • Recruiting Zn2+ to mediate potent, specific inhibition of serine proteases.

    abstract::As regulators of ubiquitous biological processes, serine proteases can cause disease states when inappropriately expressed or regulated, and are thus rational targets for inhibition by drugs. Recently we described a new inhibition mechanism applicable for the development of potent, selective small molecule serine prot...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3071

    authors: Katz BA,Luong C

    更新日期:1999-09-24 00:00:00

  • αB-crystallin polydispersity is a consequence of unbiased quaternary dynamics.

    abstract::The inherent heterogeneity of many protein assemblies complicates characterization of their structure and dynamics, as most biophysical techniques require homogeneous preparations of isolated components. For this reason, quantitative studies of the molecular chaperone αB-crystallin, which populates a range of intercon...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.07.016

    authors: Baldwin AJ,Lioe H,Robinson CV,Kay LE,Benesch JL

    更新日期:2011-10-21 00:00:00

  • Tn5 transposes independently of cointegrate resolution. Evidence for an alternative model for transposition.

    abstract::The replicon fusion model for transposition predicts that each transposable element encodes a site-specific recombination activity (resolvase). A series of experiments were performed to test for the presence of such a resolvase in Tn5. None could be found when assays were devised to detect inter- or intramolecular rec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90028-2

    authors: Isberg RR,Syvanen M

    更新日期:1985-03-05 00:00:00