当前位置： SCI文献检索 > NATURE STRUCTURAL & MOLECULAR BIOLOGY期刊下所有文献 > UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites.

UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites.

Abstract：

:Ubiquitination is a post-translational modification (PTM) that is essential for balancing numerous physiological processes. To enable delineation of protein ubiquitination at a site-specific level, we generated an antibody, denoted UbiSite, recognizing the C-terminal 13 amino acids of ubiquitin, which remain attached to modified peptides after proteolytic digestion with the endoproteinase LysC. Notably, UbiSite is specific to ubiquitin. Furthermore, besides ubiquitination on lysine residues, protein N-terminal ubiquitination is readily detected as well. By combining UbiSite enrichment with sequential LysC and trypsin digestion and high-accuracy MS, we identified over 63,000 unique ubiquitination sites on 9,200 proteins in two human cell lines. In addition to uncovering widespread involvement of this PTM in all cellular aspects, the analyses reveal an inverse association between protein N-terminal ubiquitination and acetylation, as well as a complete lack of correlation between changes in protein abundance and alterations in ubiquitination sites upon proteasome inhibition.

journal_name

Nat Struct Mol Biol

journal_title

Nature structural & molecular biology

authors

Akimov V,Barrio-Hernandez I,Hansen SVF,Hallenborg P,Pedersen AK,Bekker-Jensen DB,Puglia M,Christensen SDK,Vanselow JT,Nielsen MM,Kratchmarova I,Kelstrup CD,Olsen JV,Blagoev B

doi

10.1038/s41594-018-0084-y

subject

Has Abstract

pub_date

2018-07-01 00:00:00

pages

631-640

issue

7

eissn

1545-9993

issn

1545-9985

pii

10.1038/s41594-018-0084-y

journal_volume

25

pub_type

杂志文章

相关文献

NATURE STRUCTURAL & MOLECULAR BIOLOGY文献大全
  • The hunt for RNA polymerase II elongation factors: a historical perspective.

    abstract：:The discovery of the three eukaryotic nuclear RNA polymerases paved the way for serious biochemical investigations of eukaryotic transcription and the identification of eukaryotic transcription factors. Here we describe this adventure from our vantage point, with a focus on the hunt for factors that regulate elongatio...

    journal_title：Nature structural & molecular biology

    pub_type： 历史文章,杂志文章,评审

    doi：10.1038/s41594-019-0283-1

    authors： Conaway RC,Conaway JW

    更新日期：2019-09-01 00:00:00

  • Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.

    abstract：:It has recently been shown that RNA 3'-end formation plays a more widespread role in controlling gene expression than previously thought. To examine the impact of regulated 3'-end formation genome-wide, we applied direct RNA sequencing to A. thaliana. Here we show the authentic transcriptome in unprecedented detail an...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2345

    authors： Sherstnev A,Duc C,Cole C,Zacharaki V,Hornyik C,Ozsolak F,Milos PM,Barton GJ,Simpson GG

    更新日期：2012-08-01 00:00:00

  • Notch is a direct negative regulator of the DNA-damage response.

    abstract：:The DNA-damage response (DDR) ensures genome stability and proper inheritance of genetic information, both of which are essential to survival. It is presently unclear to what extent other signaling pathways modulate DDR function. Here we show that Notch receptor binds and inactivates ATM kinase and that this mechanism...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.3013

    authors： Vermezovic J,Adamowicz M,Santarpia L,Rustighi A,Forcato M,Lucano C,Massimiliano L,Costanzo V,Bicciato S,Del Sal G,d'Adda di Fagagna F

    更新日期：2015-05-01 00:00:00

  • Nonsense-mediated mRNA decay occurs during eIF4F-dependent translation in human cells.

    abstract：:The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs undergoing premature termination of translation. It has been argued that in human cells, NMD is restricted to a pioneer round of translation initiated on mRNAs associated with the cap-binding complex (CBC) and that the exchange of the CBC for the eIF4F tran...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2575

    authors： Durand S,Lykke-Andersen J

    更新日期：2013-06-01 00:00:00

  • Chromatin organization marks exon-intron structure.

    abstract：:An increasing body of evidence indicates that transcription and splicing are coupled, and it is accepted that chromatin organization regulates transcription. Little is known about the cross-talk between chromatin structure and exon-intron architecture. By analysis of genome-wide nucleosome-positioning data sets from h...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1659

    authors： Schwartz S,Meshorer E,Ast G

    更新日期：2009-09-01 00:00:00

  • Structural basis for midbody targeting of spastin by the ESCRT-III protein CHMP1B.

    abstract：:The endosomal sorting complex required for transport (ESCRT) machinery, including ESCRT-III, localizes to the midbody and participates in the membrane-abscission step of cytokinesis. The ESCRT-III protein charged multivesicular body protein 1B (CHMP1B) is required for recruitment of the MIT domain-containing protein s...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1512

    authors： Yang D,Rismanchi N,Renvoisé B,Lippincott-Schwartz J,Blackstone C,Hurley JH

    更新日期：2008-12-01 00:00:00

  • Defining the landscape of ATP-competitive inhibitor resistance residues in protein kinases.

    abstract：:Kinases are involved in disease development and modulation of their activity can be therapeutically beneficial. Drug-resistant mutant kinases are valuable tools in drug discovery efforts, but the prediction of mutants across the kinome is challenging. Here, we generate deep mutational scanning data to identify mutant ...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-019-0358-z

    authors： Persky NS,Hernandez D,Do Carmo M,Brenan L,Cohen O,Kitajima S,Nayar U,Walker A,Pantel S,Lee Y,Cordova J,Sathappa M,Zhu C,Hayes TK,Ram P,Pancholi P,Mikkelsen TS,Barbie DA,Yang X,Haq R,Piccioni F,Root DE,Johannes

    更新日期：2020-01-01 00:00:00

  • Autoinhibition of X11/Mint scaffold proteins revealed by the closed conformation of the PDZ tandem.

    abstract：:Members of the X11/Mint family of multidomain adaptor proteins are composed of a divergent N terminus, a conserved PTB domain and a pair of C-terminal PDZ domains. Many proteins can interact with the PDZ tandem of X11 proteins, although the mechanism of such interactions is unclear. Here we show that the highly conser...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb958

    authors： Long JF,Feng W,Wang R,Chan LN,Ip FC,Xia J,Ip NY,Zhang M

    更新日期：2005-08-01 00:00:00

  • A genome-wide map of adeno-associated virus-mediated human gene targeting.

    abstract：:To determine which genomic features promote homologous recombination, we created a genome-wide map of gene targeting sites. We used an adeno-associated virus vector to target identical loci introduced as transcriptionally active retroviral vectors. A comparison of ~2,000 targeted and untargeted sites showed that targe...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2895

    authors： Deyle DR,Hansen RS,Cornea AM,Li LB,Burt AA,Alexander IE,Sandstrom RS,Stamatoyannopoulos JA,Wei CL,Russell DW

    更新日期：2014-11-01 00:00:00

  • Conformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis.

    abstract：:The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ClpP proteolytic chamber. Here, we determined high-resolution structures of wild-type Escherichia coli ClpAP undergoing act...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-020-0409-5

    authors： Lopez KE,Rizo AN,Tse E,Lin J,Scull NW,Thwin AC,Lucius AL,Shorter J,Southworth DR

    更新日期：2020-05-01 00:00:00

  • Proton-powered subunit rotation in single membrane-bound F0F1-ATP synthase.

    abstract：:Synthesis of ATP from ADP and phosphate, catalyzed by F(0)F(1)-ATP synthases, is the most abundant physiological reaction in almost any cell. F(0)F(1)-ATP synthases are membrane-bound enzymes that use the energy derived from an electrochemical proton gradient for ATP formation. We incorporated double-labeled F(0)F(1)-...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb718

    authors： Diez M,Zimmermann B,Börsch M,König M,Schweinberger E,Steigmiller S,Reuter R,Felekyan S,Kudryavtsev V,Seidel CA,Gräber P

    更新日期：2004-02-01 00:00:00

  • Publisher Correction: Tauopathies: Protein shapes at the core of chronic traumatic encephalopathy.

    abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title：Nature structural & molecular biology

    pub_type： 已发布勘误

    doi：10.1038/s41594-019-0251-9

    authors： Fichou Y,Han S

    更新日期：2019-06-01 00:00:00

  • A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain.

    abstract：:Argonaute (Ago) proteins mediate silencing of nucleic acid targets by small RNAs. In fission yeast, Ago1, Tas3 and Chp1 assemble into a RITS complex, which silences transcription near centromeres. Here we describe a repetitive motif within Tas3, termed the 'Argonaute hook', that is conserved from yeast to humans and b...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb1302

    authors： Till S,Lejeune E,Thermann R,Bortfeld M,Hothorn M,Enderle D,Heinrich C,Hentze MW,Ladurner AG

    更新日期：2007-10-01 00:00:00

  • Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1.

    abstract：:The PHD finger protein 1 (PHF1) is essential in epigenetic regulation and genome maintenance. Here we show that the Tudor domain of human PHF1 binds to histone H3 trimethylated at Lys36 (H3K36me3). We report a 1.9-Å resolution crystal structure of the Tudor domain in complex with H3K36me3 and describe the molecular me...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2435

    authors： Musselman CA,Avvakumov N,Watanabe R,Abraham CG,Lalonde ME,Hong Z,Allen C,Roy S,Nuñez JK,Nickoloff J,Kulesza CA,Yasui A,Côté J,Kutateladze TG

    更新日期：2012-12-01 00:00:00

  • Structure-function analyses of the human SIX1-EYA2 complex reveal insights into metastasis and BOR syndrome.

    abstract：:SIX1 interacts with EYA to form a bipartite transcription factor essential for mammalian development. Loss of function of this complex causes branchio-oto-renal (BOR) syndrome, whereas re-expression of SIX1 or EYA promotes metastasis. Here we describe the 2.0-Å structure of SIX1 bound to EYA2, which suggests a new DNA...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2505

    authors： Patrick AN,Cabrera JH,Smith AL,Chen XS,Ford HL,Zhao R

    更新日期：2013-04-01 00:00:00

  • Reconstitution of anaphase DNA bridge recognition and disjunction.

    abstract：:Faithful chromosome segregation requires that the sister chromatids be disjoined completely. Defective disjunction can lead to the persistence of histone-free threads of DNA known as ultra-fine bridges (UFBs) that connect the separating sister DNA molecules during anaphase. UFBs arise at specific genomic loci and can ...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-018-0123-8

    authors： Sarlós K,Biebricher AS,Bizard AH,Bakx JAM,Ferreté-Bonastre AG,Modesti M,Paramasivam M,Yao Q,Peterman EJG,Wuite GJL,Hickson ID

    更新日期：2018-09-01 00:00:00

  • An unstructured initiation site is required for efficient proteasome-mediated degradation.

    abstract：:The proteasome is the main ATP-dependent protease in eukaryotic cells and controls the concentration of many regulatory proteins in the cytosol and nucleus. Proteins are targeted to the proteasome by the covalent attachment of polyubiquitin chains. The ubiquitin modification serves as the proteasome recognition elemen...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb814

    authors： Prakash S,Tian L,Ratliff KS,Lehotzky RE,Matouschek A

    更新日期：2004-09-01 00:00:00

  • Substrate-engaged 26S proteasome.

    abstract：: ...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-018-0167-9

    authors： Marcinkiewicz KM

    更新日期：2018-12-01 00:00:00

  • Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy.

    abstract：:Seven-helix membrane proteins represent a challenge for structural biology. Here we report the first NMR structure determination of a detergent-solubilized seven-helix transmembrane (7TM) protein, the phototaxis receptor sensory rhodopsin II (pSRII) from Natronomonas pharaonis, as a proof of principle. The overall qua...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1807

    authors： Gautier A,Mott HR,Bostock MJ,Kirkpatrick JP,Nietlispach D

    更新日期：2010-06-01 00:00:00

  • Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease.

    abstract：:DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5'-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5'-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx-DNA-AMP-Zn(2+) comple...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2146

    authors： Tumbale P,Appel CD,Kraehenbuehl R,Robertson PD,Williams JS,Krahn J,Ahel I,Williams RS

    更新日期：2011-10-09 00:00:00

  • A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain.

    abstract：:Interactions between Src homology 2 (SH2) domains and phosphotyrosine sites regulate tyrosine kinase signaling networks. Selective perturbation of these interactions is challenging due to the high homology among the 120 human SH2 domains. Using an improved phage-display selection system, we generated a small antibody ...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1793

    authors： Wojcik J,Hantschel O,Grebien F,Kaupe I,Bennett KL,Barkinge J,Jones RB,Koide A,Superti-Furga G,Koide S

    更新日期：2010-04-01 00:00:00

  • Messenger RNA interactions in the decoding center control the rate of translocation.

    abstract：:During protein synthesis, mRNA and tRNAs are iteratively translocated by the ribosome. Precisely what molecular event is rate limiting for translocation is not known. Here we show that disruption of the interactions between the A-site codon and the ribosome accelerates translocation, suggesting that the release of the...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2140

    authors： Khade PK,Joseph S

    更新日期：2011-10-23 00:00:00

  • Structure of a proton-dependent lipid transporter involved in lipoteichoic acids biosynthesis.

    abstract：:Lipoteichoic acids (LTAs) are essential cell-wall components in Gram-positive bacteria, including the human pathogen Staphylococcus aureus, contributing to cell adhesion, cell division and antibiotic resistance. Genetic evidence has suggested that LtaA is the flippase that mediates the translocation of the lipid-linke...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-020-0425-5

    authors： Zhang B,Liu X,Lambert E,Mas G,Hiller S,Veening JW,Perez C

    更新日期：2020-06-01 00:00:00

  • Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs.

    abstract：:Flavin-containing monooxygenases (FMOs) are ubiquitous in all domains of life and metabolize a myriad of xenobiotics, including toxins, pesticides and drugs. However, despite their pharmacological importance, structural information remains bereft. To further our understanding behind their biochemistry and diversity, w...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-019-0347-2

    authors： Nicoll CR,Bailleul G,Fiorentini F,Mascotti ML,Fraaije MW,Mattevi A

    更新日期：2020-01-01 00:00:00

  • Transcription shapes DNA replication initiation and termination in human cells.

    abstract：:Although DNA replication is a fundamental aspect of biology, it is not known what determines where DNA replication starts and stops in the human genome. We directly identified and quantitatively compared sites of replication initiation and termination in untransformed human cells. We found that replication preferentia...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-018-0171-0

    authors： Chen YH,Keegan S,Kahli M,Tonzi P,Fenyö D,Huang TT,Smith DJ

    更新日期：2019-01-01 00:00:00

  • Active site remodeling switches HIV specificity of antiretroviral TRIMCyp.

    abstract：:TRIMCyps are primate antiretroviral proteins that potently inhibit HIV replication. Here we describe how rhesus macaque TRIMCyp (RhTC) has evolved to target and restrict HIV-2. We show that the ancestral cyclophilin A (CypA) domain of RhTC targets HIV-2 capsid with weak affinity, which is strongly increased in RhTC by...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1667

    authors： Price AJ,Marzetta F,Lammers M,Ylinen LM,Schaller T,Wilson SJ,Towers GJ,James LC

    更新日期：2009-10-01 00:00:00

  • Energetics of ångström-scale conformational changes in an RCK domain of the MthK K+ channel.

    abstract：:Allosteric proteins transition among different conformational states in a ligand-dependent manner. Upon resolution of a protein's individual states, one can determine the probabilities of these states, thereby dissecting the energetic mechanisms underlying their conformational changes. Here we examine individual regul...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-019-0275-1

    authors： Lewis JH,Lu Z

    更新日期：2019-09-01 00:00:00

  • Structural analysis of the interaction between Hsp90 and the tumor suppressor protein p53.

    abstract：:In eukaryotes, the essential dimeric molecular chaperone Hsp90 is required for the activation and maturation of specific substrates such as steroid hormone receptors, tyrosine kinases and transcription factors. Hsp90 is involved in the establishment of cancer and has become an attractive target for drug design. Here w...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2114

    authors： Hagn F,Lagleder S,Retzlaff M,Rohrberg J,Demmer O,Richter K,Buchner J,Kessler H

    更新日期：2011-09-04 00:00:00

  • Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.

    abstract：:Despite growing appreciation of the importance of long noncoding RNAs (lncRNAs) in normal physiology and disease, our knowledge of cancer-related lncRNAs remains limited. By repurposing microarray probes, we constructed expression profiles of 10,207 lncRNA genes in approximately 1,300 tumors over four different cancer...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2591

    authors： Du Z,Fei T,Verhaak RG,Su Z,Zhang Y,Brown M,Chen Y,Liu XS

    更新日期：2013-07-01 00:00:00

  • Structural basis for protein-RNA recognition in telomerase.

    abstract：:Telomerase is a large ribonucleoprotein complex minimally composed of a catalytic telomerase reverse transcriptase (TERT) and an RNA component (TR) that provides the template for telomeric DNA synthesis. However, it remains unclear how TERT and TR assemble into a functional telomerase. Here we report the crystal struc...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2819

    authors： Huang J,Brown AF,Wu J,Xue J,Bley CJ,Rand DP,Wu L,Zhang R,Chen JJ,Lei M

    更新日期：2014-06-01 00:00:00