A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods.

Abstract:

:Different bioinformatics methods illuminate different aspects of protein function, from specific catalytic activities to broad functional categories. Here, a triple-pronged approach to predict function for a domain of unknown function, DUF2086, is applied. Distant homology to characterised enzymes and conservation of key residues suggest an oxygenase function. Modelling indicates that the substrate is most likely a nucleic acid. Finally, genomic context analysis linking DUF2086 to DNA repair, leads to a predicted activity of oxidative demethylation of damaged bases in DNA. The newly assigned activity is sporadically present in phyla not containing near relatives of the similarly active repair protein AlkB.

journal_name

FEBS Lett

journal_title

FEBS letters

authors

Mello LV,Rigden DJ

doi

10.1016/j.febslet.2012.09.023

subject

Has Abstract

pub_date

2012-11-02 00:00:00

pages

3908-13

issue

21

eissn

0014-5793

issn

1873-3468

pii

S0014-5793(12)00731-4

journal_volume

586

pub_type

杂志文章
  • SRTX-d, a new native peptide of the endothelin/sarafotoxin family.

    abstract::The primary structure of a new sarafotoxin, SRTX-d, from the venom of Atractaspis engaddensis is described. SRTX-d differs from SRTX-b in two substitutions: Ile19 instead of Val and Thr2 instead of Ser. The toxicity of SRTX-d and its vasoconstriction potency are very low in comparison to SRTX-a and SRTX-b, whereas its...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(89)81706-5

    authors: Bdolah A,Wollberg Z,Fleminger G,Kochva E

    更新日期:1989-10-09 00:00:00

  • Over-expression of FoxM1 stimulates cyclin B1 expression.

    abstract::FoxM1 (previously named WIN, HFH-11 or Trident) is a Forkhead box (Fox) transcription factor widely expressed in proliferating cells. Various findings, including a recent analysis of FoxM1 knockout mice, suggest that FoxM1 is required for normal S-M coupling during cell cycle progression. To study the regulatory role ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(01)02915-5

    authors: Leung TW,Lin SS,Tsang AC,Tong CS,Ching JC,Leung WY,Gimlich R,Wong GG,Yao KM

    更新日期:2001-10-19 00:00:00

  • Regulation of the F0F1-ATP synthase: the conformation of subunit epsilon might be determined by directionality of subunit gamma rotation.

    abstract::F(0)F(1)-ATP synthase couples ATP synthesis/hydrolysis with transmembrane proton transport. The catalytic mechanism involves rotation of the gamma epsilon c(approximately 10)-subunits complex relative to the rest of the enzyme. In the absence of protonmotive force the enzyme is inactivated by the tight binding of MgAD...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/j.febslet.2005.08.030

    authors: Feniouk BA,Junge W

    更新日期:2005-09-26 00:00:00

  • Acylation of adenylyl cyclase catalyst is important for enzymic activity.

    abstract::Incubation of human thrombocytes in the presence of [3H]palmitic acid leads to incorporation of this fatty acid into the alpha subunit of Gs as described [Linder et al., Proc. Natl. Acad. Sci. USA 90 (1993) 3675-3679; Degtyarev et al., Biochemistry 32 (1993) 8057-8061] but also into the catalyst of adenylyl cyclase wh...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(95)00864-6

    authors: Mollner S,Beck K,Pfeuffer T

    更新日期:1995-09-11 00:00:00

  • Intracellular Ca2+ can compensate for the lack of NADPH oxidase-derived ROS in endothelial cells.

    abstract::The aim of the present study is to determine the role of intracellular Ca(2+) in VEGF signaling. We demonstrate that reduction in Ca(2+) by chelating compound BAPTA-AM or by IP(3)-endoplasmic reticulum blocker 2-APB selectively inhibited VEGF-induced activation of c-Src-PI3K-Akt but not ERK1/2 in human coronary artery...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2010.05.053

    authors: Lee M,Spokes KC,Aird WC,Abid MR

    更新日期:2010-07-16 00:00:00

  • YDL142c encodes cardiolipin synthase (Cls1p) and is non-essential for aerobic growth of Saccharomyces cerevisiae.

    abstract::The unassigned open reading frame YDL142c was identified to code for cardiolipin synthase, Cls1p. A cls1 deletion strain is viable on glucose, galactose, ethanol, glycerol and lactate containing media, although the growth rate on non-fermentable carbon sources is decreased. Mitochondria of the cls1 mutant are devoid o...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)01525-1

    authors: Tuller G,Hrastnik C,Achleitner G,Schiefthaler U,Klein F,Daum G

    更新日期:1998-01-02 00:00:00

  • Fc epsilon receptor mediated Ca2+ influx into mast cells is modulated by the concentration of cytosolic free Ca2+ ions.

    abstract::The relationship between the Fc epsilon receptor mediated stimulation of mast cells and the Ca2+ signal it induces were studied using thapsigargin (TG), a blocker of the endoplasmic reticulum Ca2+ pump. TG induced, in mucosal mast cells (RBL-2H3 line), a dose-dependent and an InsP3-independent increase in [Ca2+]i (fro...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(92)81311-9

    authors: Dar O,Pecht I

    更新日期:1992-09-28 00:00:00

  • Cooperativity and flexibility of active sites in homodimeric transketolase.

    abstract::Here we summarize evidence for non-equivalence of two structurally similar active sites in transketolase and other thiamine-dependent enzymes. This non-equivalence takes place when the enzymes interact with various ligands (inhibitors, cations, coenzyme and substrates). Data on different strains in the structure of th...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(98)01423-9

    authors: Kovina MV,Kochetov GA

    更新日期:1998-11-27 00:00:00

  • Carbohydrate-induced modulation of cell membrane. VIII. Agglutination with mammalian lectin galectin-1 increases osmofragility and membrane fluidity of trypsinized erythrocytes.

    abstract::Interaction of lectins with cell surface determinants may alter membrane properties. Using trypsinized rabbit erythrocytes as model we tested the capacity of an endogenous lectin in this respect. Galectin-1 is a member of an adhesion/growth-regulatory family known to interact for example with ganglioside GM(1) and als...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2006.02.006

    authors: Gupta RK,Pande AH,Gulla KC,Gabius HJ,Hajela K

    更新日期:2006-03-06 00:00:00

  • Utilization of alanine for glucose formation in isolated rabbit kidney-cortex tubules.

    abstract::In kidney cortex tubules isolated from fed rabbits L-alanine is not utilized as glucose precursor, when added as a sole substrate. However, this amino acid decreases gluconeogenesis from low (up to 1 mM) 2-oxoglutarate concentrations and stimulates this process at higher (2.5-10 mM) ketoacid contents in the suspension...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(89)81514-5

    authors: Zabłocki K,Bryła J

    更新日期:1989-12-18 00:00:00

  • Abeta production as consequence of cellular death of a human neuroblastoma overexpressing APP.

    abstract::In human brain the Abeta peptide is produced mainly by neurons and the overexpression of amyloid precursor protein (APP) that involves an increase in Abeta secretion, has been observed in some areas of the Alzheimer's disease patients brain. We have generated two stably transfected human neuroblastoma lines which over...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2004.06.025

    authors: Recuero M,Serrano E,Bullido MJ,Valdivieso F

    更新日期:2004-07-16 00:00:00

  • Cloning and expression of a bovine adenylyl cyclase type VII specific to the retinal pigment epithelium.

    abstract::A cDNA of a type 7 adenylyl cyclase isoform was cloned from a bovine retinal pigment epithelium cDNA library using oligonucleotides developed to conserved regions common to mammalian adenylyl cyclases. A 6.7 kb mRNA of very high abundance was uniquely present on Northern blots containing mRNA or total RNA from the pig...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(95)01470-5

    authors: Völkel H,Beitz E,Klumpp S,Schultz JE

    更新日期:1996-01-15 00:00:00

  • A reporter for dsRNA response in Neurospora crassa.

    abstract::In the filamentous fungus Neurospora, the production of dsRNA can elicit a dsRNA-induced transcriptional response similar to the interferon response in vertebrates. However, how fungi sense the expression of dsRNA and activate gene expression is unknown. In this study, we established a dsRNA response reporter system i...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2011.02.024

    authors: Li X,Shen Y,Sun J,Wang B,He Q

    更新日期:2011-03-23 00:00:00

  • Structural characteristics and refolding of in vivo aggregated hyperthermophilic archaeon proteins.

    abstract::Several recombinant proteins in inclusion bodies expressed in Escherichia coli have been measured by Fourier transform infrared and solid-state nuclear magnetic resonance spectra to provide the secondary structural characteristics of the proteins from hyperthermophilic archaeon Pyrococcus horikoshii OT3 (hyperthermoph...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(03)01441-8

    authors: Umetsu M,Tsumoto K,Ashish K,Nitta S,Tanaka Y,Adschiri T,Kumagai I

    更新日期:2004-01-16 00:00:00

  • Molecular cloning and expression of a new alpha-subunit of soluble guanylyl cyclase. Interchangeability of the alpha-subunits of the enzyme.

    abstract::A cDNA coding for a new subunit of soluble guanylyl cyclase with a calculated molecular mass of 81.7 kDa was cloned and sequenced. On the basis of sequence homology, the new subunit appears to be an isoform of the alpha 1-subunit and was designated alpha 2 as the new subunit is very similar to the alpha 1-subunit in t...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(91)80871-y

    authors: Harteneck C,Wedel B,Koesling D,Malkewitz J,Böhme E,Schultz G

    更新日期:1991-11-04 00:00:00

  • Translational fusion of heat labile enterotoxin chain B and beta-subunit of human chorionic gonadotropin: periplasmic expression in Escherichia coli and its immunogenicity.

    abstract::A fusion gene was constructed consisting of heat labile enterotoxin chain B (LTB) of E. coli genetically linked at its C-terminus to the beta-subunit of human chorionic gonadotropin in translational fusion, under the control of tac promoter and LTB signal sequence. Expression of the fusion gene (about 5 microgram/ml) ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(96)00428-0

    authors: Pillai D,Dixit A,Alok D,Garg LC

    更新日期:1996-05-27 00:00:00

  • Maturation and degradation of beta-galactosidase in the post-Golgi compartment are regulated by cathepsin B and a non-cysteine protease.

    abstract::Lysosomal beta-galactosidase precursor is processed to a mature form and associated with protective protein in lysosomes. In this study we used two cysteine protease proinhibitors, E64-d for cathepsins B, S, H, and L, and CA074Me for cathepsin B. They are converted intracellularly to active forms, E-64c and CA074, res...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)01461-0

    authors: Okamura-Oho Y,Zhang S,Callahan JW,Murata M,Oshima A,Suzuki Y

    更新日期:1997-12-15 00:00:00

  • Estramustine phosphate but not estramustine inhibits the interaction of microtubule associated protein 2 (MAP2) with actin filaments.

    abstract::The effect of estramustine and estramustine phosphate (EP) on the interaction of microtubule associated protein 2 (MAP2) with actin has been examined. We show that (a) neither estramustine nor EP influences actin polymerisation (b) EP, but not estramustine, reduces the amount of MAP2 which co-sediments with F-actin in...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(96)01524-4

    authors: Pedrotti B,Islam K

    更新日期:1997-02-17 00:00:00

  • Identification and characterization of Runx2 phosphorylation sites involved in matrix metalloproteinase-13 promoter activation.

    abstract::Matrix metalloproteinase-13 (MMP-13) plays a critical role in parathyroid hormone (PTH)-induced bone resorption. PTH acts via protein kinase A (PKA) to phosphorylate and stimulate the transactivation of Runx2 for MMP-13 promoter activation. We show here that PTH stimulated Runx2 phosphorylation in rat osteoblastic cel...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2009.02.040

    authors: Selvamurugan N,Shimizu E,Lee M,Liu T,Li H,Partridge NC

    更新日期:2009-04-02 00:00:00

  • Tertiary structural models for human interleukin-6 and evaluation by a sequence-structure compatibility method and NMR experimental information.

    abstract::Tertiary structure models of Interleukin-6 were constructed using a routine prediction method based on the X-ray crystal structures of granulocyte colony-stimulating factor (GCSF) and leukemia inhibitory factor (LIF). The models were evaluated with the aid of the sequence-structure compatibility (3D-1D) method program...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)00115-4

    authors: Sumikawa H,Fukuhara K,Suzuki E,Matsuo Y,Nishikawa K

    更新日期:1997-03-10 00:00:00

  • Affinity labelling of Escherichia coli ribosomes with a benzylidene derivative of AUGU6 within initiation and pretranslocational complexes.

    abstract::Affinity labelling of E. coli ribosomes with the 2',3'-O-[4-(N-2-chloroethyl)-N-methylamino]benzylidene derivative of AUGU6 was studied within the initiation complex (complex I) obtained by using fMet-tRNAMetf and initiation factors and within the pretranslocational complex (complex II) obtained by treatment of comple...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(86)80714-1

    authors: Babkina GT,Veniaminova AG,Vladimirov SN,Karpova GG,Yamkovoy VI,Berzin VA,Gren EJ,Cielens IE

    更新日期:1986-07-07 00:00:00

  • A mutation which disrupts the hydrophobic core of the signal peptide of bilirubin UDP-glucuronosyltransferase, an endoplasmic reticulum membrane protein, causes Crigler-Najjar type II.

    abstract::Crigler-Najjar (CN) disease is caused by a deficiency of the hepatic enzyme, bilirubin UDP-glucuronosyltransferase (B-UGT). We have found two CN type II patients, who were homozygous for a leucine to arginine transition at position 15 of B-UGT1. This mutation is expected to disrupt the hydrophobic core of the signal p...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(96)00677-1

    authors: Seppen J,Steenken E,Lindhout D,Bosma PJ,Elferink RP

    更新日期:1996-07-29 00:00:00

  • The DNA sequence specificity of cyanomorpholinoadriamycin.

    abstract::Cyanomorpholinoadriamycin (1 microM) was reacted in a transcription buffer with DNA of an initiated transcription complex. Subsequent elongation of the initiated complex revealed permanent transcriptional blockages at 16 sites after only 5 min of drug-DNA reaction time. The most dominant sites were immediately prior t...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(91)81185-b

    authors: Cullinane C,Phillips DR

    更新日期:1991-11-18 00:00:00

  • A genetic approach to elucidating eukaryotic iron metabolism.

    abstract::Studies of mutants of the yeast Saccharomyces cerevisiae have led to the identification of genes required for high affinity iron uptake. Reduction of iron (III) outside the cell is accomplished by means of reductases encoded by FRE1 and FRE2, homologues of the gp91-phox component of the oxygen reductase of human granu...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/0014-5793(94)01111-7

    authors: Klausner RD,Dancis A

    更新日期:1994-11-28 00:00:00

  • GLUT4 translocation by insulin in intact muscle cells: detection by a fast and quantitative assay.

    abstract::We report a rapid and sensitive colorimetric approach to quantitate the amount of glucose transporters exposed at the surface of intact cells, using L6 muscle cells expressing GLUT4 containing an exofacial myc epitope. Unstimulated cells exposed to the surface 5 fmol GLUT4myc per mg protein. This value increased to 10...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(98)00423-2

    authors: Wang Q,Khayat Z,Kishi K,Ebina Y,Klip A

    更新日期:1998-05-08 00:00:00

  • Direct protein-protein interactions and substrate channeling between cellular retinoic acid binding proteins and CYP26B1.

    abstract::Cellular retinoic acid binding proteins (CRABPs) bind all-trans-retinoic acid (atRA) tightly. This study aimed to determine whether atRA is channeled directly to cytochrome P450 (CYP) CYP26B1 by CRABPs, and whether CRABPs interact directly with CYP26B1. atRA bound to CRABPs (holo-CRABP) was efficiently metabolized by ...

    journal_title:FEBS letters

    pub_type: 信件

    doi:10.1002/1873-3468.12303

    authors: Nelson CH,Peng CC,Lutz JD,Yeung CK,Zelter A,Isoherranen N

    更新日期:2016-08-01 00:00:00

  • MiR-449c targets c-Myc and inhibits NSCLC cell progression.

    abstract::MicroRNAs (miRNA) play an important role in tumorigenesis, proliferation, and differentiation. Altered miRNA expression in cancer indicates that miRNAs can function as tumor suppressors or oncogenes. MiR-449c downregulation in non-small cell lung cancer (NSCLC) compared with normal lung tissues was investigated in thi...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2013.03.006

    authors: Miao LJ,Huang SF,Sun ZT,Gao ZY,Zhang RX,Liu Y,Wang J

    更新日期:2013-05-02 00:00:00

  • Purification and functional characterization of beta-adrenergic receptor kinase expressed in insect cells.

    abstract::The beta-adrenergic receptor kinase mediates agonist-dependent phosphorylation of beta-adrenergic receptors, which is thought to represent the first step of homologous desensitization. We have expressed bovine and human beta ARK1 in Sf9 cells and purified them to apparent homogeneity in milligram quantities. The Km-va...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(93)81532-5

    authors: Söhlemann P,Hekman M,Buchen C,Elce JS,Lohse MJ

    更新日期:1993-06-07 00:00:00

  • Calcium-induced calcium release mediated by a voltage-activated cation channel in vacuolar vesicles from red beet.

    abstract::Little is known about the mechanisms underlying calcium-induced Ca2+ release (CICR) in plants. The slow-activating vacuolar (SV) channel is both permeable to, and activated by Ca2+, and is therefore a prime candidate for a role in CICR. Cytosol-side-out vacuolar membrane vesicles loaded with 45Ca2+ showed voltage- and...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(99)01109-6

    authors: Bewell MA,Maathuis FJ,Allen GJ,Sanders D

    更新日期:1999-09-10 00:00:00

  • Beta-glucosidase activity towards a bile acid glucoside in human liver.

    abstract::Human liver contains hydrolytic activity toward 3 beta-glucosido-chenodeoxycholic acid. This beta-glucosidase activity, localized predominantly in the microsomal fraction, was optimally active in the presence of divalent metal ions close to pH 5.0 and was inhibited by EDTA. Kinetic parameters and other catalytic prope...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(92)80970-r

    authors: Matern H,Gartzen R,Matern S

    更新日期:1992-12-14 00:00:00