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 adjacent PHD finger remains unclear. Here, we report the high-resolution crystal structure of UHRF1 PHD finger in complex with N-terminal tail of histone H3. We found that the preceding zinc-Cys4 knuckle is indispensable for the PHD finger of UHRF1 to recognize the first four unmodified residues of histone H3 N-terminal tail. Quantitative binding studies indicated that UHRF1 PHD finger (including the preceding zinc-Cys4 knuckle) acts together with the adjacent double Tudor domain to specifically recognize the H3K9me3 mark. Combinatorial recognition of H3K9me3-containing histone H3 tail by UHRF1 PHD finger and double Tudor domain may play a role in establishing and maintaining histone H3K9 methylation patterns during the cell cycle.

journal_name

J Mol Biol

authors

Xie S,Jakoncic J,Qian C

doi

10.1016/j.jmb.2011.11.012

subject

Has Abstract

pub_date

2012-01-13 00:00:00

pages

318-28

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(11)01231-9

journal_volume

415

pub_type

杂志文章
  • Modular architecture of the hexameric human mitochondrial DNA helicase.

    abstract::We have probed the structure of the human mitochondrial DNA helicase, an enzyme that uses the energy of nucleotide hydrolysis to unwind duplex DNA during mitochondrial DNA replication. This novel helicase shares substantial amino acid sequence and functional similarities with the bacteriophage T7 primase-helicase. We ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.01.079

    authors: Ziebarth TD,Farr CL,Kaguni LS

    更新日期:2007-04-13 00:00:00

  • Crystal structures of Enoyl-ACP reductases I (FabI) and III (FabL) from B. subtilis.

    abstract::Enoyl-[acyl carrier protein] (ACP) reductase (ENR) is a key enzyme in type II fatty acid synthesis that catalyzes the last step in each elongation cycle. Therefore, it has been considered as a target for antibiotics. However, recent studies indicate that some pathogens have more than one ENR; in particular, Bacillus s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.12.003

    authors: Kim KH,Ha BH,Kim SJ,Hong SK,Hwang KY,Kim EE

    更新日期:2011-02-25 00:00:00

  • Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages.

    abstract::AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.08.025

    authors: Shishovs M,Rumnieks J,Diebolder C,Jaudzems K,Andreas LB,Stanek J,Kazaks A,Kotelovica S,Akopjana I,Pintacuda G,Koning RI,Tars K

    更新日期:2016-10-23 00:00:00

  • The replisome organizer (G38P) of Bacillus subtilis bacteriophage SPP1 forms specialized nucleoprotein complexes with two discrete distant regions of the SPP1 genome.

    abstract::Initiation of Bacillus subtilis bacteriophage SPP1 DNA replication requires the products of genes 38, 39 and 40 (G38P, G39P and G40P). G38P specifically binds two discrete regions, which are 32.1 kb apart in a linear map of the SPP1 genome. One of these target sites, which maps at the left end of the phage genome, wit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1060

    authors: Missich R,Weise F,Chai S,Lurz R,Pedré X,Alonso JC

    更新日期:1997-07-04 00:00:00

  • Internal promoter elements of transfer RNA genes are preferentially exposed in chromatin.

    abstract::We have examined the chromatin organization of a cluster of transfer RNA genes at the cytogenic locus 90BC on the right arm of the third Drosophila melanogaster chromosome. We find that the internal promoter sequences are preferentially exposed to micrococcal nuclease and DNase I in chromatin. Moreover, these exposed ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90158-x

    authors: DeLotto R,Schedl P

    更新日期:1984-11-15 00:00:00

  • Non-proteolytic functions of calpain-3 in sarcoplasmic reticulum in skeletal muscles.

    abstract::Mutations in CAPN3/Capn3, which codes for skeletal muscle-specific calpain-3/p94 protease, are responsible for limb-girdle muscular dystrophy type 2A. Using "knock-in" (referred to as Capn3(CS/CS)) mice, in which the endogenous calpain-3 is replaced with a mutant calpain-3:C129S, which is a proteolytically inactive bu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.01.057

    authors: Ojima K,Ono Y,Ottenheijm C,Hata S,Suzuki H,Granzier H,Sorimachi H

    更新日期:2011-04-01 00:00:00

  • The crystal and molecular structure of the Rhizomucor miehei triacylglyceride lipase at 1.9 A resolution.

    abstract::The crystal and molecular structure of a triacylglyceride lipase (EC 3.1.1.3) from the fungus Rhizomucor miehei was analyzed using X-ray single crystal diffraction data to 1.9 A resolution. The structure was refined to an R-factor of 0.169 for all available data. The details of the molecular architecture and the cryst...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90225-9

    authors: Derewenda ZS,Derewenda U,Dodson GG

    更新日期:1992-10-05 00:00:00

  • Structure of short thick filaments from Limulus muscle.

    abstract::Shortened Limulus thick filaments, isolated from stimulated muscle, are structurally similar to long filaments, isolated from unstimulated muscle, except for length. Both have 3-fold screw symmetry with a helical repeat at approximately 43 nm, axial spacing of 14.5 nm between successive crowns of crossbridges and 4-fo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90351-1

    authors: Levine RJ,Kensler RW

    更新日期:1985-03-20 00:00:00

  • A structural model for the DEAD box helicase YxiN in solution: localization of the RNA binding domain.

    abstract::DEAD box proteins consist of a common helicase core formed by two globular RecA domains that are separated by a cleft. The helicase core acts as a nucleotide-dependent switch that alternates between open and closed conformations during the catalytic cycle of duplex separation, thereby providing basic helicase activity...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.07.049

    authors: Karow AR,Klostermeier D

    更新日期:2010-10-01 00:00:00

  • Architecture of the Complex Formed by Large and Small Terminase Subunits from Bacteriophage P22.

    abstract::Packaging of viral genomes inside empty procapsids is driven by a powerful ATP-hydrolyzing motor, formed in many double-stranded DNA viruses by a complex of a small terminase (S-terminase) subunit and a large terminase (L-terminase) subunit, transiently docked at the portal vertex during genome packaging. Despite rece...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.08.013

    authors: McNulty R,Lokareddy RK,Roy A,Yang Y,Lander GC,Heck AJR,Johnson JE,Cingolani G

    更新日期:2015-10-09 00:00:00

  • Kinetic buffering of cross talk between bacterial two-component sensors.

    abstract::Two-component systems are a class of sensors that enable bacteria to respond to environmental and cell-state signals. The canonical system consists of a membrane-bound sensor histidine kinase that autophosphorylates in response to a signal and transfers the phosphate to an intracellular response regulator. Bacteria ty...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.05.007

    authors: Groban ES,Clarke EJ,Salis HM,Miller SM,Voigt CA

    更新日期:2009-07-17 00:00:00

  • Conformation of BCL-XL upon Membrane Integration.

    abstract::BCL-XL is an anti-apoptotic BCL-2 family protein found both in the cytosol and bound to intracellular membranes. Structural studies of BCL-XL have advanced by deleting its hydrophobic C-terminus and adding detergents to enhance solubility. However, since the C-terminus is essential for function and detergents strongly...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.02.019

    authors: Yao Y,Fujimoto LM,Hirshman N,Bobkov AA,Antignani A,Youle RJ,Marassi FM

    更新日期:2015-07-03 00:00:00

  • Early events in the binding of the pPS10 replication protein RepA to single iteron and operator DNA sequences.

    abstract::RepA protein, encoded in the Pseudomonas pPS10 replicon, is a stable dimer in solution (dRepA), acting as a self-repressor of repA transcription through binding to an inverted repeat operator. However, RepA monomers (mRepA) are required to initiate plasmid replication upon binding to four directly repeated DNA sequenc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.09.013

    authors: Díaz-López T,Dávila-Fajardo C,Blaesing F,Lillo MP,Giraldo R

    更新日期:2006-12-15 00:00:00

  • Crystallization of halophilic malate dehydrogenase from Halobacterium marismortui.

    abstract::Malate dehydrogenase from the extreme halophile Halobacterium marismortui crystallizes in highly concentrated phosphate solution in space group 12 with cell dimensions a = 113.8 A, b = 122.8 A, c = 126.7 A, beta = 98.1 degrees. The halophilic enzyme was found to be unstable at lower concentrations of phosphate. It ass...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90547-5

    authors: Harel M,Shoham M,Frolow F,Eisenberg H,Mevarech M,Yonath A,Sussman JL

    更新日期:1988-04-05 00:00:00

  • pK values of histidine residues in ribonuclease Sa: effect of salt and net charge.

    abstract::The primary goal of this study was to gain a better understanding of the effect of environment and ionic strength on the pK values of histidine residues in proteins. The salt-dependence of pK values for two histidine residues in ribonuclease Sa (RNase Sa) (pI=3.5) and a variant in which five acidic amino acids have be...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01274-3

    authors: Huyghues-Despointes BM,Thurlkill RL,Daily MD,Schell D,Briggs JM,Antosiewicz JM,Pace CN,Scholtz JM

    更新日期:2003-01-31 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

  • Limited proteolysis unmasks specific DNA-binding of the murine RNA polymerase I-specific transcription termination factor TTFI.

    abstract::Previously we have shown that nuclear extracts from mouse cells contain a heterogeneous group of polypeptides (p65, p80, p90, p100) which form distinct DNA-protein complexes on the 18 base-pair sequence element (termed Sal-box), which constitutes the murine rDNA transcription termination signal. These distinct protein...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90213-4

    authors: Smid A,Finsterer M,Grummt I

    更新日期:1992-10-05 00:00:00

  • Molecular analysis of mutations in the hprt gene of V79 hamster fibroblasts: effects of imbalances in the dCTP, dGTP and dTTP pools.

    abstract::dCMP-deaminase-deficient V79/dC hamster cells have highly imbalanced deoxyribonucleoside triphosphate (dNTP) pools, i.e. a 17-fold larger dCTP pool, a slightly reduced dTTP and a very low dGTP pool, compared to dCMP-deaminase-proficient V79/p cells. Nevertheless, the two lines showed the same rates of spontaneous muta...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0516

    authors: Darè E,Zhang LH,Jenssen D,Bianchi V

    更新日期:1995-10-06 00:00:00

  • prlF and yhaV encode a new toxin-antitoxin system in Escherichia coli.

    abstract::Toxin-antitoxin systems consist of a stable toxin, frequently with endonuclease activity, and a small, labile antitoxin, which sequesters the toxin into an inactive complex. Under unfavorable conditions, the antitoxin is degraded, leading to activation of the toxin and resulting in growth arrest, possibly also in bact...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.07.016

    authors: Schmidt O,Schuenemann VJ,Hand NJ,Silhavy TJ,Martin J,Lupas AN,Djuranovic S

    更新日期:2007-09-28 00:00:00

  • Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI.

    abstract::The restriction enzyme R.BbvCI cleaves duplex DNA within a seven base-pair asymmetric recognition sequence, thus: CCTCAGC/GCTGAGG-->CC--TCAGC/GC--TGAGG. We show that R.BbvCI comprises two different subunits, R(1) and R(2); that each subunit contains a catalytic site for DNA strand hydrolysis; and that these sites act ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.02.034

    authors: Heiter DF,Lunnen KD,Wilson GG

    更新日期:2005-05-06 00:00:00

  • Studies of the hyperthermophile Thermotoga maritima by random sequencing of cDNA and genomic libraries. Identification and sequencing of the trpEG (D) operon.

    abstract::Random sequencing of cDNA and genomic libraries has been used to study the genome of the hyperthermophile Thermotoga maritima. To date, 175 unique clones have been analyzed by comparing short sequence tags with known proteins in the PIR and GenBank databases. We find that a significant proportion of sequences can be m...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1345

    authors: Kim CW,Markiewicz P,Lee JJ,Schierle CF,Miller JH

    更新日期:1993-06-20 00:00:00

  • Structural effect of complete [Rp]-phosphorothioate and phosphorodithioate substitutions in the DNA strand of a model antisense inhibitor-target RNA complex.

    abstract::Chemically modified DNA oligonucleotides have been crucial to the success of antisense therapeutics. Although such modifications are ubiquitous in the clinic, high-resolution structural studies of pharmaceutically relevant derivatives have been limited to only a few molecules. We have completed a high-resolution NMR s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2305

    authors: Furrer P,Billeci TM,Donati A,Kojima C,Karwowski B,Sierzchala A,Stec W,James TL

    更新日期:1999-01-29 00:00:00

  • Insights into RNA virus mutant spectrum and lethal mutagenesis events: replicative interference and complementation by multiple point mutants.

    abstract::RNA virus behavior can be influenced by interactions among viral genomes and their expression products within the mutant spectra of replicating viral quasispecies. Here, we report the extent of interference of specific capsid and polymerase mutants of foot-and-mouth disease virus (FMDV) on replication of wild-type (wt...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.03.074

    authors: Perales C,Mateo R,Mateu MG,Domingo E

    更新日期:2007-06-15 00:00:00

  • Crystallographic structure of phosphofructokinase-2 from Escherichia coli in complex with two ATP molecules. Implications for substrate inhibition.

    abstract::Phosphofructokinase-1 and -2 (Pfk-1 and Pfk-2, respectively) from Escherichia coli belong to different homologous superfamilies. However, in spite of the lack of a common ancestor, they share the ability to catalyze the same reaction and are inhibited by the substrate MgATP. Pfk-2, an ATP-dependent 6-phosphofructokina...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.08.029

    authors: Cabrera R,Ambrosio AL,Garratt RC,Guixé V,Babul J

    更新日期:2008-11-14 00:00:00

  • A dimer is the minimal proton-conducting unit of the influenza a virus M2 channel.

    abstract::When influenza A virus infects host cells, its integral matrix protein M2 forms a proton-selective channel in the viral envelope. Although X-ray crystallography and NMR studies using fragment peptides have suggested that M2 stably forms a tetrameric channel irrespective of pH, the oligomeric states of the full-length ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.05.002

    authors: Kawano K,Yano Y,Matsuzaki K

    更新日期:2014-07-15 00:00:00

  • Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

    abstract::Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small, fast-folding proteins. To investigate the extent of the topological control of the folding process, we studied the folding of simplified models ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3693

    authors: Clementi C,Nymeyer H,Onuchic JN

    更新日期:2000-05-19 00:00:00

  • Distinct modes of recognition of the lipoyl domain as substrate by the E1 and E3 components of the pyruvate dehydrogenase multienzyme complex.

    abstract::Two-dimensional (15)N-heteronuclear single-quantum coherence (HSQC) NMR studies with a di-domain (lipoyl domain+ linker+ peripheral subunit-binding domain) of the dihydrolipoyl acetyltransferase (E2) component of the pyruvate dehydrogenase complex of Bacillus stearothermophilus allowed a molecular comparison of the ne...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.11.018

    authors: Fries M,Stott KM,Reynolds S,Perham RN

    更新日期:2007-02-09 00:00:00

  • DNA curvature in native and modified EcoRI recognition sites and possible influence upon the endonuclease cleavage reaction.

    abstract::The ligation of a decadeoxynucleotide containing the EcoRI recognition site forms a series of multimers which appear to be curved based on observed anomalous gel migration in polyacrylamide gels. The degree of DNA curvature present in the recognition sequence, based upon the observed migration anomaly, can be altered ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90561-x

    authors: Diekmann S,McLaughlin LW

    更新日期:1988-08-20 00:00:00

  • On the role of alphaThr183 in the allosteric regulation and catalytic mechanism of tryptophan synthase.

    abstract::The catalytic activity and substrate channeling of the pyridoxal 5'-phosphate-dependent tryptophan synthase alpha(2)beta(2) complex is regulated by allosteric interactions that modulate the switching of the enzyme between open, low activity and closed, high activity states during the catalytic cycle. The highly conser...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01109-9

    authors: Kulik V,Weyand M,Seidel R,Niks D,Arac D,Dunn MF,Schlichting I

    更新日期:2002-12-06 00:00:00

  • Structural analysis of the human fibroblast growth factor receptor 4 kinase.

    abstract::The family of fibroblast growth factor receptors (FGFRs) plays an important and well-characterized role in a variety of pathological disorders. FGFR4 is involved in myogenesis and muscle regeneration. Mutations affecting the kinase domain of FGFR4 may cause cancer, for example, breast cancer or rhabdomyosarcoma. Where...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.09.004

    authors: Lesca E,Lammens A,Huber R,Augustin M

    更新日期:2014-11-11 00:00:00