Abstract：
:The three-dimensional structure of Aspergillus aculeatus beta-1,4-galactanase (AAGAL), an enzyme involved in pectin degradation, has been determined by multiple isomorphous replacement to 2.3 and 1.8 A resolution at 293 and 100 K, respectively. It represents the first known structure for a polysaccharidase with this specificity and for a member of glycoside hydrolase family 53 (GH-53). The enzyme folds into a (beta/alpha)(8) barrel with the active site cleft located at the C-terminal side of the barrel consistent with the classification of GH-53 in clan GH-A, a superfamily of enzymes with common fold and catalytic machinery but diverse specificities. Putative substrate-enzyme interactions were elucidated by modeling of beta-1,4-linked galactobioses into the possible substrate binding subsites. The structure and modeling studies identified five potential subsites for the binding of galactans, of which one is a pocket suited for accommodating the arabinan side chain in arabinogalactan, one of the natural substrates. A comparison with the substrate binding grooves of other Clan GH-A enzymes suggests that shape complementarity is crucial in determining the specificity of polysaccharidases.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Ryttersgaard C,Lo Leggio L,Coutinho PM,Henrissat B,Larsen Sdoi
10.1021/bi026238csubject
Has Abstractpub_date
2002-12-24 00:00:00pages
15135-43issue
51eissn
0006-2960issn
1520-4995pii
bi026238cjournal_volume
41pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:Colibactins are genotoxic secondary metabolites whose biosynthesis is encoded in the clb gene cluster harbored by certain strains of gut commensal Escherichia coli. Using synthetic colibactin analogues, we previously provided evidence that colibactins alkylate DNA by addition of a nucleotide to an electrophilic cyclop...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.8b01023
更新日期：2018-11-13 00:00:00
abstract：:Binding mechanisms of ADPR-transferase to restricted double-stranded DNA fragments of SV40 and pBR322 DNA were determined by nuclease protection techniques. Top and bottom strands of double-stranded DNA were identified by specific labeling with 32P. Protection against specific exonucleases identified binding of ADPR-t...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00439a050
更新日期：1989-06-27 00:00:00
abstract：:Quantum tunneling and protein dynamics have emerged as important components of enzyme function. This review focuses on soybean lipoxygenase-1, to illustrate how the properties of enzymatic C-H bond activation link protein motions to the fundamental bond making-breaking processes. ...
journal_title：Biochemistry
pub_type： 杂志文章,评审
doi：10.1021/bi301504m
更新日期：2013-03-26 00:00:00
abstract：:The HpxO enzyme from Klebsiella pneumoniae was recently proposed, on the basis of genetic studies, to catalyze the hydroxylation of uric acid to 5-hydroxyisourate as part of the purine catabolic pathway. Its primary sequence suggests that the HpxO catalytic activity depends on a flavin cofactor (FAD), contrasting with...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi900160b
更新日期：2009-04-14 00:00:00
abstract：:KCNE1 is a single transmembrane protein that modulates the function of voltage-gated potassium channels, including KCNQ1. Hereditary mutations in the genes encoding either protein can result in diseases such as congenital deafness, long QT syndrome, ventricular tachyarrhythmia, syncope, and sudden cardiac death. Despi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.5b00505
更新日期：2015-10-20 00:00:00
abstract：:HpaI and BphI are two pyruvate class II aldolases found in aromatic meta-cleavage degradation pathways that catalyze similar reactions but are not related in sequence. Steady-state kinetic analysis of the aldol addition reactions and product inhibition assays showed that HpaI exhibits a rapid equilibrium random order ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi100251u
更新日期：2010-05-04 00:00:00
abstract：:The mechanisms for substrate recognition by two cytoplasmic protein tyrosine phosphatases, PTP-5 and rrbPTP-1, were investigated. Phosphorylation sites on tyrosine-phosphorylated casein, a model PTP substrate, were characterized. Two peptides based on casein phosphorylation sites and one peptide based on the tyrosine ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00097a019
更新日期：1993-11-23 00:00:00
abstract：:The inheritance of DNA methylation patterns may play an important role in the stability of the differentiated state. We have therefore studied the inhibitory effects of DNA binding proteins on DNA methylation in vitro. Mouse L1210 cells grown in the presence of 5-azacytidine acquire hemimethylated sites in their DNA. ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00326a021
更新日期：1985-02-26 00:00:00
abstract：:Electron spin polarized electron paramagentic resonance (ESP EPR) spectra were obtained with deuterated iron-removed photosynthetic bacterial reaction centers (RCs) to specifically investigate the effect of the rate of primary charge separation, metal-site occupancy, and H-subunit content on the observed P865+QA- char...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9630319
更新日期：1997-07-15 00:00:00
abstract：:Inosine has the ability to act as a "wild-card" binding nonspecifically to both A.T and G.C base pairs. This has obvious implications for the design of oligonucleotide site-directed probes. In this paper we present a series of oligonucleotides with a 5'pur9-pyr9-pyr9 motif which are designed to fold up sequentially in...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi960193w
更新日期：1996-10-15 00:00:00
abstract：:The orientation of eukaryotic cytochromes P450, with respect to the membrane of the endoplasmic reticulum, has been investigated. There is now good evidence that the tertiary structure of these proteins is essentially the same as that of the soluble bacterial isoenzyme cytochrome P450CI, with the exception of an exten...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00215a011
更新日期：1991-01-08 00:00:00
abstract：:Ca2+-induced fusion of phospholipid vesicles (phosphatidylcholine/phosphatidic acid, 9:1 mol/mol) prepared by ethanolic injection was followed by five different procedures: resonance energy transfer, light scattering, electron microscopy, intermixing of aqueous content, and gel filtration through Sepharose 4-B. The fi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00329a015
更新日期：1985-04-09 00:00:00
abstract：:A description of the efficient high-level expression of the monomer hemoglobin (GMG4) from Glycera dibranchiata is presented. The cDNA described by Simons and Satterlee [Simons, P.C., & Satterlee, J.D. (1989) Biochemistry 28, 8525-8530] was subcloned into an expression system, and conditions were found that led to the...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00200a014
更新日期：1994-08-30 00:00:00
abstract：:Genomic clones encompassing all the translated sequences, the 3' untranslated sequence, and 1 kb flanking the ATG translation initiation codon of bovine tropoelastin have been obtained and characterized by restriction enzyme analysis and extensive DNA sequencing. These analyses demonstrated that functionally distinct ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00432a003
更新日期：1989-03-21 00:00:00
abstract：:Eukaryotic transfer RNA precursors (pre-tRNAs) contain a 5' leader preceding the aminoacyl acceptor stem and a 3' trailer extending beyond this stem. An early step in pre-tRNA maturation is removal of the 5' leader by the endoribonuclease, RNase P. Extensive pairing between leader and trailer sequences has previously ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi000603n
更新日期：2000-08-15 00:00:00
abstract：:The low level of enzymatic activity of certain alpha 2-macroglobulin-proteinase complexes could be important to the function of factor VIII/von Willebrand glycoprotein since it is especially sensitive to proteolytic cleavage. To test this possibility, complexes of alpha 2-macroglobulin with plasmin, trypsin, and throm...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00275a018
更新日期：1983-03-15 00:00:00
abstract：:Previously [Luz et al. (1994) Biochemistry 33, 7239-7249], we determined that Cl(-)- and -HCO3-dependent pHi homeostasis was perturbed in multidrug resistant (MDR) cells created by transfecting LR73 Chinese hamster ovary fibroblasts with wild-type mu (murine) MDR 1 (Gros et al., 1991). Via single-cell photometry exper...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00202a021
更新日期：1994-09-13 00:00:00
abstract：:To identify residues and segments in the central region of apolipoprotein A-I (apoA-I) that are important for the protein structure and stability, we studied the effects of four double charge ablations, D102A/D103A, E110A/E111A, R116V/K118A, and R160V/H162A, and two deletion mutations, Delta(61-78) and Delta(121-142),...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi051669r
更新日期：2006-01-31 00:00:00
abstract：:Retinoid X receptors (RXRs) are nuclear receptors that can activate transcription as homodimers or as obligate heterodimeric partners of other nuclear receptors. While the crystal structures of the RXR ligand-binding domains (LBD) have been previously determined, the dynamics of activation is less well characterized a...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi051474j
更新日期：2006-02-14 00:00:00
abstract：:The amino acids (residues 39-51) responsible for the interaction between the first intracellular loop (iLP1) of the human prostacyclin receptor (IP) and G alpha s protein have been identified [Zhang, L., Huang, G., Wu, J., and Ruan, K. H. (2005) Biochemistry 44, 11389-11401]. To further characterize the structural/fun...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0515669
更新日期：2006-02-14 00:00:00
abstract：:The DeltaG degrees (N)(-)(D) value obtained from extrapolation to zero denaturant concentration by the linear extrapolation method (LEM) is commonly interpreted to represent the Gibbs energy difference between native (N) and denatured (D) ensembles at the limit of zero denaturant concentration. For DeltaG degrees (N)(...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi001071d
更新日期：2000-12-12 00:00:00
abstract：:The chromatin structure encompassing the lysozyme gene domain in hen oviduct nuclei was studied by measuring the partitioning of coding and flanking sequences during chromatin fractionation and by analyzing the nucleosome repeat in response to micrococcal nuclease digestion. Following micrococcal nuclease digestion, n...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00350a033
更新日期：1986-01-28 00:00:00
abstract：:Isoforms of transforming growth factor beta (TGFbeta) are 25 kDa homodimeric polypeptides that signal by binding and bringing together two related, functionally distinct cell surface receptors designated as TbetaR1 and TbetaR2. Here, we report the solution structure of the 13.8 kDa extracellular domain of human TbetaR...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi034366a
更新日期：2003-09-02 00:00:00
abstract：:The thermal denaturation of the cupredoxin plastocyanin (PC) from spinach has been studied with the aim of improving the understanding of factors involved in the conformational stability of antiparallel beta-sheet proteins. Studies using differential scanning calorimetry have been complemented with nuclear magnetic re...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi034371e
更新日期：2003-09-02 00:00:00
abstract：:We examined the metabolism of exogenously added 13C-labeled fructose 1,6-bisphosphate (either labeled at the first and sixth carbons or labeled at the first carbon only) and of [2-13C]glucose in well-oxygenated and well-superfused hog carotid artery segments. Exogenously added fructose 1,6-bisphosphate was utilized by...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00004a027
更新日期：1995-01-31 00:00:00
abstract：:Effects of paramagnetic shift reagents on the 13C NMR spectra obtained from single-walled vesicle dispersions of egg phosphatidylcholine enriched with 13C in the N-methyl carbons are investigated. Spectra obtained at 25.1 MHz show that, at Yb3+ to phospholipid molar ratios as low as 0.06, complete resolution of the N-...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00653a007
更新日期：1976-04-20 00:00:00
abstract：:To shed more light on the molecular requirements for recognition of thyroid response elements (TREs) by thyroid receptors (TRs), we compared the specific aspects of DNA TRE recognition by different TR constructs. Using fluorescence anisotropy, we performed a detailed and hierarchical study of TR-TRE binding. This was ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi901282s
更新日期：2010-02-09 00:00:00
abstract：:In an effort to further probe metal binding to metallo-beta-lactamase L1 (mbetal L1), Cu- (Cu-L1) and Ni-substituted (Ni-L1) L1 were prepared and characterized by kinetic and spectroscopic studies. Cu-L1 bound 1.7 equiv of Cu and small amounts of Zn(II) and Fe. The EPR spectrum of Cu-L1 exhibited two overlapping, axia...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi802295z
更新日期：2009-04-07 00:00:00
abstract：:Phosphoenolthiopyruvate, the analogue of phosphoenolpyruvate in which the bridging oxygen of the phosphate ester is replaced by sulfur, has been synthesized from methyl acrylate and dimethyl (chlorothio)phosphonate. The compound is a substrate for alkaline phosphatase, pyruvate kinase, enolase, and phosphoenolpyruvate...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00404a038
更新日期：1988-02-23 00:00:00
abstract：:Helicobacter pylori NikR (HpNikR) is a nickel-responsive transcription factor. In addition to a role in nickel homeostasis, HpNikR is proposed to serve as a master activator-repressor for H. pylori acid adaptation by directly or indirectly regulating the expression of a battery of genes. One potential mechanism of thi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi801742r
更新日期：2009-03-24 00:00:00
