Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates.

Abstract:

:SUMO processing and deconjugation are essential proteolytic activities for nuclear metabolism and cell-cycle progression in yeast and higher eukaryotes. To elucidate the mechanisms used during substrate lysine deconjugation, SUMO isoform processing and SUMO isoform interactions, X-ray structures were determined for a catalytically inert SENP2 protease domain in complex with conjugated RanGAP1-SUMO-1 or RanGAP1-SUMO-2, or in complex with SUMO-2 or SUMO-3 precursors. Common features within the active site include a 90 degrees kink proximal to the scissile bond that forces C-terminal amino acid residues or the lysine side chain toward a protease surface that appears optimized for lysine deconjugation. Analysis of this surface reveals SENP2 residues, particularly Met497, that mediate, and in some instances reverse, in vitro substrate specificity. Mutational analysis and biochemistry provide a mechanism for SENP2 substrate preferences that explains why SENP2 catalyzes SUMO deconjugation more efficiently than processing.

journal_name

Nat Struct Mol Biol

authors

Reverter D,Lima CD

doi

10.1038/nsmb1168

subject

Has Abstract

pub_date

2006-12-01 00:00:00

pages

1060-8

issue

12

eissn

1545-9993

issn

1545-9985

pii

nsmb1168

journal_volume

13

pub_type

杂志文章
  • Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction.

    abstract::We have determined the solution structure of the complex between an arginine-glycine-rich RGG peptide from the human fragile X mental retardation protein (FMRP) and an in vitro-selected guanine-rich (G-rich) sc1 RNA. The bound RNA forms a newly discovered G-quadruplex separated from the flanking duplex stem by a mixed...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.2064

    authors: Phan AT,Kuryavyi V,Darnell JC,Serganov A,Majumdar A,Ilin S,Raslin T,Polonskaia A,Chen C,Clain D,Darnell RB,Patel DJ

    更新日期:2011-06-05 00:00:00

  • Complex interactions between the DNA-damage response and mammalian telomeres.

    abstract::Natural chromosome ends resemble double-stranded DNA breaks, but they do not activate a damage response in healthy cells. Telomeres therefore have evolved to solve the 'end-protection problem' by inhibiting multiple DNA damage-response pathways. During the past decade, the view of telomeres has progressed from simple ...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章,评审

    doi:10.1038/nsmb.3092

    authors: Arnoult N,Karlseder J

    更新日期:2015-11-01 00:00:00

  • The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle.

    abstract::The N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown. The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylat...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.2641

    authors: Arnaudo N,Fernández IS,McLaughlin SH,Peak-Chew SY,Rhodes D,Martino F

    更新日期:2013-09-01 00:00:00

  • Allosteric inhibition of protein tyrosine phosphatase 1B.

    abstract::Obesity and type II diabetes are closely linked metabolic syndromes that afflict >100 million people worldwide. Although protein tyrosine phosphatase 1B (PTP1B) has emerged as a promising target for the treatment of both syndromes, the discovery of pharmaceutically acceptable inhibitors that bind at the active site re...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb803

    authors: Wiesmann C,Barr KJ,Kung J,Zhu J,Erlanson DA,Shen W,Fahr BJ,Zhong M,Taylor L,Randal M,McDowell RS,Hansen SK

    更新日期:2004-08-01 00:00:00

  • An assessment of histone-modification antibody quality.

    abstract::We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibo...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1972

    authors: Egelhofer TA,Minoda A,Klugman S,Lee K,Kolasinska-Zwierz P,Alekseyenko AA,Cheung MS,Day DS,Gadel S,Gorchakov AA,Gu T,Kharchenko PV,Kuan S,Latorre I,Linder-Basso D,Luu Y,Ngo Q,Perry M,Rechtsteiner A,Riddle NC,Schwar

    更新日期:2011-01-01 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

  • Rps26 directs mRNA-specific translation by recognition of Kozak sequence elements.

    abstract::We describe a novel approach to separate two ribosome populations from the same cells and use this method in combination with RNA-seq to identify mRNAs bound to Saccharomyces cerevisiae ribosomes with and without Rps26, a protein linked to the pathogenesis of Diamond-Blackfan anemia (DBA). These analyses reveal that R...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.3442

    authors: Ferretti MB,Ghalei H,Ward EA,Potts EL,Karbstein K

    更新日期:2017-09-01 00:00:00

  • Author Correction: Structural basis for polyglutamate chain initiation and elongation by TTLL family enzymes.

    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/s41594-020-0498-1

    authors: Mahalingan KK,Keith Keenan E,Strickland M,Li Y,Liu Y,Ball HL,Tanner ME,Tjandra N,Roll-Mecak A

    更新日期:2020-09-01 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

  • Membrane-dependent conformational changes initiate cholesterol-dependent cytolysin oligomerization and intersubunit beta-strand alignment.

    abstract::Cholesterol-dependent cytolysins are bacterial protein toxins that bind to cholesterol-containing membranes, form oligomeric complexes and insert into the bilayer to create large aqueous pores. Membrane-dependent structural rearrangements required to initiate the oligomerization of perfringolysin O monomers have been ...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb793

    authors: Ramachandran R,Tweten RK,Johnson AE

    更新日期:2004-08-01 00:00:00

  • Structure of the Dom34-Hbs1 complex and implications for no-go decay.

    abstract::No-go decay (NGD) targets mRNAs with stalls in translation elongation for endonucleolytic cleavage in a process involving the Dom34 and Hbs1 proteins. The crystal structure of a Schizosaccharomyces pombe Dom34-Hbs1 complex reveals an overall shape similar to that of eRF1-eRF3-GTP and EF-Tu-tRNA-GDPNP. Similarly to eRF...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1922

    authors: Chen L,Muhlrad D,Hauryliuk V,Cheng Z,Lim MK,Shyp V,Parker R,Song H

    更新日期:2010-10-01 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

  • Regulation of MLL1 H3K4 methyltransferase activity by its core components.

    abstract::Histone H3 Lys4 (H3K4) methylation is a prevalent mark associated with transcription activation. A common feature of several H3K4 methyltransferase complexes is the presence of three structural components (RbBP5, Ash2L and WDR5) and a catalytic subunit containing a SET domain. Here we report the first biochemical reco...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1128

    authors: Dou Y,Milne TA,Ruthenburg AJ,Lee S,Lee JW,Verdine GL,Allis CD,Roeder RG

    更新日期:2006-08-01 00:00:00

  • ERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane.

    abstract::Ribosomes translating secretory and membrane proteins are targeted to the endoplasmic reticulum membrane and attach to the protein-conducting channel and ribosome-associated membrane proteins (RAMPs). Recently, a new RAMP, ERj1p, has been identified that recruits BiP to ribosomes and regulates translational activity. ...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb998

    authors: Blau M,Mullapudi S,Becker T,Dudek J,Zimmermann R,Penczek PA,Beckmann R

    更新日期:2005-11-01 00:00:00

  • Conformational restriction blocks glutamate receptor desensitization.

    abstract::Desensitization is a universal feature of ligand-gated ion channels. Using the crystal structure of the GluR2 L483Y mutant channel as a guide, we attempted to build non-desensitizing kainate-subtype glutamate receptors. Success was achieved for GluR5, GluR6 and GluR7 with intermolecular disulfide cross-links but not b...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1178

    authors: Weston MC,Schuck P,Ghosal A,Rosenmund C,Mayer ML

    更新日期:2006-12-01 00:00:00

  • The stoichiometry of Gag protein in HIV-1.

    abstract::The major structural components of HIV-1 are encoded as a single polyprotein, Gag, which is sufficient for virus particle assembly. Initially, Gag forms an approximately spherical shell underlying the membrane of the immature particle. After proteolytic maturation of Gag, the capsid (CA) domain of Gag reforms into a c...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb785

    authors: Briggs JA,Simon MN,Gross I,Kräusslich HG,Fuller SD,Vogt VM,Johnson MC

    更新日期:2004-07-01 00:00:00

  • RNA polymerase II C-terminal domain mediates regulation of alternative splicing by SRp20.

    abstract::Previous studies have linked the C-terminal domain (CTD) of RNA polymerase II (pol II) with cotranscriptional precursor messenger RNA processing, but little is known about the CTD's function in regulating alternative splicing. We have examined this function using alpha-amanitin-resistant pol II CTD mutants and fibrone...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1155

    authors: de la Mata M,Kornblihtt AR

    更新日期:2006-11-01 00:00:00

  • Author Correction: Musashi 1 regulates the timing and extent of meiotic mRNA translational activation by promoting the use of specific CPEs.

    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/s41594-019-0272-4

    authors: Weill L,Belloc E,Castellazzi CL,Méndez R

    更新日期:2019-08-01 00:00:00

  • Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome.

    abstract::The noncoding RNA Xist recruits silencing factors to the inactive X chromosome (Xi) and facilitates re-organization of Xi structure. Here, we examine the mouse epigenomic landscape of Xi and assess how Xist alters chromatin accessibility. Xist deletion triggers a gain of accessibility of select chromatin regions that ...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/s41594-018-0176-8

    authors: Jégu T,Blum R,Cochrane JC,Yang L,Wang CY,Gilles ME,Colognori D,Szanto A,Marr SK,Kingston RE,Lee JT

    更新日期:2019-02-01 00:00:00

  • Author Correction: A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos.

    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/s41594-019-0367-y

    authors: Putnam A,Cassani M,Smith J,Seydoux G

    更新日期:2020-02-01 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

  • Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo.

    abstract::We present the first large-scale identification of lariats-the transient branched introns that are released as a byproduct of pre-mRNA splicing. The locations of the branchpoints in these introns provide insight into the early steps of splicing. From this data set, we have developed a comprehensive model of 3' splice-...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.2327

    authors: Taggart AJ,DeSimone AM,Shih JS,Filloux ME,Fairbrother WG

    更新日期:2012-06-17 00:00:00

  • Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast.

    abstract::The RNA-induced transcriptional silencing (RITS) complex, containing Ago1, Chp1, Tas3 and centromeric small interfering RNAs (siRNAs), is required for heterochromatic gene silencing at centromeres. Here, we identify a second fission yeast Argonaute complex (Argonaute siRNA chaperone, ARC), which contains, in addition ...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1211

    authors: Buker SM,Iida T,Bühler M,Villén J,Gygi SP,Nakayama J,Moazed D

    更新日期:2007-03-01 00:00:00

  • Ligand-induced rearrangement of the dimeric metabotropic glutamate receptor 1alpha.

    abstract::The extracellular domain of the metabotropic glutamate receptor 1alpha (mGluR1alpha) forms a dimer and the ligand, glutamate, induces a structural rearrangement in this domain. However, the conformational change in the cytoplasmic domain, which is critical for mGluR1alpha's interaction with G proteins, remains unclear...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb770

    authors: Tateyama M,Abe H,Nakata H,Saito O,Kubo Y

    更新日期:2004-07-01 00:00:00

  • MacroH2A1.1 and PARP-1 cooperate to regulate transcription by promoting CBP-mediated H2B acetylation.

    abstract::The histone variant macroH2A1 regulates gene expression important for differentiation, stem-cell reprogramming and tumor suppression. Here, we demonstrate that in primary human cells, macroH2A1 participates in two physically and functionally distinct types of chromatin marked by either H3K27me3 or nine histone acetyla...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.2903

    authors: Chen H,Ruiz PD,Novikov L,Casill AD,Park JW,Gamble MJ

    更新日期:2014-11-01 00:00:00

  • Single-molecule analysis of protein-free U2-U6 snRNAs.

    abstract::Spliceosomes catalyze the maturation of precursor mRNAs in organisms ranging from yeast to humans. Their catalytic core comprises three small nuclear RNAs (U2, U5 and U6) involved in substrate positioning and catalysis. It has been postulated, but never shown experimentally, that the U2-U6 complex adopts at least two ...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1672

    authors: Guo Z,Karunatilaka KS,Rueda D

    更新日期:2009-11-01 00:00:00

  • Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing.

    abstract::We investigated whether a continuous transcript is necessary for co-transcriptional pre-mRNA processing. Cutting an intron with the fast-cleaving hepatitis delta ribozyme, but not the slower hammerhead, inhibited splicing. Therefore, exon tethering to RNA polymerase II (Pol II) cannot rescue splicing of a transcript s...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1652

    authors: Fong N,Ohman M,Bentley DL

    更新日期:2009-09-01 00:00:00

  • Author Correction: Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2.

    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/s41594-020-00527-9

    authors: Huo J,Le Bas A,Ruza RR,Duyvesteyn HME,Mikolajek H,Malinauskas T,Tan TK,Rijal P,Dumoux M,Ward PN,Ren J,Zhou D,Harrison PJ,Weckener M,Clare DK,Vogirala VK,Radecke J,Moynié L,Zhao Y,Gilbert-Jaramillo J,Knight ML,Tr

    更新日期:2020-11-01 00:00:00

  • Dynamically driven protein allostery.

    abstract::Allosteric interactions are typically considered to proceed through a series of discrete changes in bonding interactions that alter the protein conformation. Here we show that allostery can be mediated exclusively by transmitted changes in protein motions. We have characterized the negatively cooperative binding of cA...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1132

    authors: Popovych N,Sun S,Ebright RH,Kalodimos CG

    更新日期:2006-09-01 00:00:00

  • Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism.

    abstract::Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large l...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/s41594-020-0457-x

    authors: Lee BG,Merkel F,Allegretti M,Hassler M,Cawood C,Lecomte L,O'Reilly FJ,Sinn LR,Gutierrez-Escribano P,Kschonsak M,Bravo S,Nakane T,Rappsilber J,Aragon L,Beck M,Löwe J,Haering CH

    更新日期:2020-08-01 00:00:00