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Article: New roles for SUMO-targeted ubiquitin ligases in genome stability

Heideker, Christine Johanna

2014 Volume 29, Issue 1, Page(s) 38

Language	German ; English
Document type	Article
ZDB-ID	382906-6
ISSN	0179-6372
Database	Current Contents Medicine

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Article ; Online: DUBs, the regulation of cell identity and disease.

Heideker, Johanna / Wertz, Ingrid E

The Biochemical journal

2015 Volume 465, Issue 1, Page(s) 1–26

Abstract: The post-translational modification of proteins with ubiquitin represents a complex signalling system that co-ordinates essential cellular functions, including proteolysis, DNA repair, receptor signalling and cell communication. DUBs (deubiquitinases), ... ...

Abstract	The post-translational modification of proteins with ubiquitin represents a complex signalling system that co-ordinates essential cellular functions, including proteolysis, DNA repair, receptor signalling and cell communication. DUBs (deubiquitinases), the enzymes that disassemble ubiquitin chains and remove ubiquitin from proteins, are central to this system. Reflecting the complexity and versatility of ubiquitin signalling, DUB activity is controlled in multiple ways. Although several lines of evidence indicate that aberrant DUB function may promote human disease, the underlying molecular mechanisms are often unclear. Notwithstanding, considerable interest in DUBs as potential drug targets has emerged over the past years. The future success of DUB-based therapy development will require connecting the basic science of DUB function and enzymology with drug discovery. In the present review, we discuss new insights into DUB activity regulation and their links to disease, focusing on the role of DUBs as regulators of cell identity and differentiation, and discuss their potential as emerging drug targets.
MeSH term(s)	Animals ; Cells/enzymology ; Cells/pathology ; Disease ; Humans ; Substrate Specificity ; Ubiquitin-Specific Proteases/metabolism
Chemical Substances	Ubiquitin-Specific Proteases (EC 3.4.19.12)
Language	English
Publishing date	2015-01-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BJ20140496
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Article ; Online: Phosphatases, DNA damage checkpoints and checkpoint deactivation.

Heideker, Johanna / Lis, Ewa T / Romesberg, Floyd E

Cell cycle (Georgetown, Tex.)

2007 Volume 6, Issue 24, Page(s) 3058–3064

Abstract: Cells have evolved intricate and specialized responses to DNA damage, central to which are the DNA damage checkpoints that arrest cell cycle progression and facilitate the repair process. Activation of these damage checkpoints relies heavily on the ... ...

Abstract	Cells have evolved intricate and specialized responses to DNA damage, central to which are the DNA damage checkpoints that arrest cell cycle progression and facilitate the repair process. Activation of these damage checkpoints relies heavily on the activity of Ser/Thr kinases, such as Chk1 and Chk2 (Saccharomyces cerevisiae Rad53), which are themselves activated by phosphorylation. Only more recently have we begun to understand how cells disengage the checkpoints to reenter the cell cycle. Here, we review progress toward understanding the functions of phosphatases in checkpoint deactivation in S. cerevisiae, focusing on the non-redundant roles of the type 2A phosphatase Pph3 and the PP2C phosphatases Ptc2 and Ptc3 in the deactivation of Rad53. We discuss how these phosphatases may specifically recognize different phosphorylated forms of Rad53 and how each may independently regulate different facets of the checkpoint response. In conjunction with the independent dephosphorylation of other checkpoint proteins, such regulation may allow a more tailored response to DNA damage that is coordinated with the repair process, ultimately resulting in the resumption of growth.
MeSH term(s)	Animals ; Cell Cycle/physiology ; Checkpoint Kinase 1 ; Checkpoint Kinase 2 ; DNA Damage/physiology ; Humans ; Phosphoprotein Phosphatases/metabolism ; Phosphorylation ; Protein Kinases/metabolism ; Protein Phosphatase 2C ; Protein-Serine-Threonine Kinases/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins ; Protein Kinases (EC 2.7.-) ; Checkpoint Kinase 2 (EC 2.7.1.11) ; CHEK1 protein, human (EC 2.7.11.1) ; CHEK2 protein, human (EC 2.7.11.1) ; Checkpoint Kinase 1 (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; PPH3 protein, S cerevisiae (EC 3.1.3.16) ; PTC3 protein, S cerevisiae (EC 3.1.3.16) ; Phosphoprotein Phosphatases (EC 3.1.3.16) ; Protein Phosphatase 2C (EC 3.1.3.16)
Language	English
Publishing date	2007-09-20
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2146183-1
ISSN	1551-4005 ; 1538-4101 ; 1554-8627
ISSN (online)	1551-4005
ISSN	1538-4101 ; 1554-8627
DOI	10.4161/cc.6.24.5100
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Article ; Online: Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes.

Hewings, David S / Heideker, Johanna / Ma, Taylur P / AhYoung, Andrew P / El Oualid, Farid / Amore, Alessia / Costakes, Gregory T / Kirchhofer, Daniel / Brasher, Bradley / Pillow, Thomas / Popovych, Nataliya / Maurer, Till / Schwerdtfeger, Carsten / Forrest, William F / Yu, Kebing / Flygare, John / Bogyo, Matthew / Wertz, Ingrid E

Nature communications

2018 Volume 9, Issue 1, Page(s) 1162

Abstract: Activity-based probes (ABPs) are widely used to monitor the activity of enzyme families in biological systems. Inferring enzyme activity from probe reactivity requires that the probe reacts with the enzyme at its active site; however, probe-labeling ... ...

Abstract	Activity-based probes (ABPs) are widely used to monitor the activity of enzyme families in biological systems. Inferring enzyme activity from probe reactivity requires that the probe reacts with the enzyme at its active site; however, probe-labeling sites are rarely verified. Here we present an enhanced chemoproteomic approach to evaluate the activity and probe reactivity of deubiquitinase enzymes, using bioorthogonally tagged ABPs and a sequential on-bead digestion protocol to enhance the identification of probe-labeling sites. We confirm probe labeling of deubiquitinase catalytic Cys residues and reveal unexpected labeling of deubiquitinases on non-catalytic Cys residues and of non-deubiquitinase proteins. In doing so, we identify ZUFSP (ZUP1) as a previously unannotated deubiquitinase with high selectivity toward cleaving K63-linked chains. ZUFSP interacts with and modulates ubiquitination of the replication protein A (RPA) complex. Our reactive-site-centric chemoproteomics method is broadly applicable for identifying the reaction sites of covalent molecules, which may expand our understanding of enzymatic mechanisms.
MeSH term(s)	Biocatalysis ; Catalytic Domain ; Cysteine/chemistry ; Cysteine/metabolism ; Deubiquitinating Enzymes/chemistry ; Deubiquitinating Enzymes/classification ; Deubiquitinating Enzymes/genetics ; Deubiquitinating Enzymes/metabolism ; HEK293 Cells ; HeLa Cells ; Humans ; Lysine/chemistry ; Lysine/metabolism ; Molecular Probes ; Protein Processing, Post-Translational ; Proteomics/methods ; Replication Protein A/genetics ; Replication Protein A/metabolism ; Staining and Labeling/methods ; Sumoylation ; Ubiquitination
Chemical Substances	Molecular Probes ; RPA1 protein, human ; Replication Protein A ; Deubiquitinating Enzymes (EC 3.4.19.12) ; ZUP1 protein, human (EC 3.4.19.12) ; Lysine (K3Z4F929H6) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2018-03-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2041-1723
ISSN (online)	2041-1723
DOI	10.1038/s41467-018-03511-6
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Article ; Online: SUMO-targeted ubiquitin ligase, Rad60, and Nse2 SUMO ligase suppress spontaneous Top1-mediated DNA damage and genome instability.

Heideker, Johanna / Prudden, John / Perry, J Jefferson P / Tainer, John A / Boddy, Michael N

PLoS genetics

2011 Volume 7, Issue 3, Page(s) e1001320

Abstract: Through as yet undefined proteins and pathways, the SUMO-targeted ubiquitin ligase (STUbL) suppresses genomic instability by ubiquitinating SUMO conjugated proteins and driving their proteasomal destruction. Here, we identify a critical function for ... ...

Abstract	Through as yet undefined proteins and pathways, the SUMO-targeted ubiquitin ligase (STUbL) suppresses genomic instability by ubiquitinating SUMO conjugated proteins and driving their proteasomal destruction. Here, we identify a critical function for fission yeast STUbL in suppressing spontaneous and chemically induced topoisomerase I (Top1)-mediated DNA damage. Strikingly, cells with reduced STUbL activity are dependent on tyrosyl-DNA phosphodiesterase 1 (Tdp1). This is notable, as cells lacking Tdp1 are largely aphenotypic in the vegetative cell cycle due to the existence of alternative pathways for the removal of covalent Top1-DNA adducts (Top1cc). We further identify Rad60, a SUMO mimetic and STUbL-interacting protein, and the SUMO E3 ligase Nse2 as critical Top1cc repair factors in cells lacking Tdp1. Detection of Top1ccs using chromatin immunoprecipitation and quantitative PCR shows that they are elevated in cells lacking Tdp1 and STUbL, Rad60, or Nse2 SUMO ligase activity. These unrepaired Top1ccs are shown to cause DNA damage, hyper-recombination, and checkpoint-mediated cell cycle arrest. We further determine that Tdp1 and the nucleotide excision repair endonuclease Rad16-Swi10 initiate the major Top1cc repair pathways of fission yeast. Tdp1-based repair is the predominant activity outside S phase, likely acting on transcription-coupled Top1cc. Epistasis analyses suggest that STUbL, Rad60, and Nse2 facilitate the Rad16-Swi10 pathway, parallel to Tdp1. Collectively, these results reveal a unified role for STUbL, Rad60, and Nse2 in protecting genome stability against spontaneous Top1-mediated DNA damage.
MeSH term(s)	Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; DNA Adducts/genetics ; DNA Adducts/metabolism ; DNA Damage/genetics ; DNA Repair ; DNA Topoisomerases, Type I/genetics ; DNA Topoisomerases, Type I/metabolism ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Genomic Instability ; Phosphoric Diester Hydrolases/genetics ; Phosphoric Diester Hydrolases/metabolism ; SUMO-1 Protein/genetics ; SUMO-1 Protein/metabolism ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; Signal Transduction ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Chromosomal Proteins, Non-Histone ; DNA Adducts ; Fungal Proteins ; Nse2 protein, S pombe ; RAD16 protein, S pombe ; Rad60 protein, S pombe ; SUMO-1 Protein ; Schizosaccharomyces pombe Proteins ; Tdp1 protein, S pombe ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Phosphoric Diester Hydrolases (EC 3.1.4.-) ; DNA Topoisomerases, Type I (EC 5.99.1.2)
Language	English
Publishing date	2011-03-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1001320
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Article: Crystal structure of archaeal ribonuclease P protein aRpp29 from Archaeoglobus fulgidus.

Sidote, David J / Heideker, Johanna / Hoffman, David W

Biochemistry

2004 Volume 43, Issue 44, Page(s) 14128–14138

Abstract: The crystal structure of ribonuclease P protein aRpp29 from the sulfate-reducing hyperthermophile Archaeoglobus fulgidus was determined at 1.7 A resolution using X-ray diffraction methods. The central feature of this archaeal protein is a sheet of six ... ...

Abstract	The crystal structure of ribonuclease P protein aRpp29 from the sulfate-reducing hyperthermophile Archaeoglobus fulgidus was determined at 1.7 A resolution using X-ray diffraction methods. The central feature of this archaeal protein is a sheet of six antiparallel beta-strands twisted around a conserved hydrophobic core. Residues near the N- and C-termini form helical structures that are oriented in an antiparallel manner. A comparison of conserved amino acids indicates that archaeal aRpp29 is homologous to human ribonuclease P protein Rpp29. The aRpp29 protein is structurally similar to bacterial transcription factors Hfq and NusG, as well as the Sm and Sm-like RNA-associated proteins from eukarya. The crystal structure of A. fulgidus aRpp29 differs from the previously reported solution structure, where NMR data did not detect the helices and indicated that approximately 40% of the residues are relatively flexible or disordered. Circular dichroism data indicate that the protein has less helical content than the amount observed in the crystal, suggesting that in solution the helical regions are unfolded or in equilibrium between folded and unfolded forms; this hypothesis is consistent with amide proton exchange rate data. Surface residues that are conserved from archaea to humans and are likely to interact with the ribonuclease P RNA or other protein subunits are identified in the structure. The model of the aRpp29 protein defined by this work provides an essential step toward eventually understanding the overall architecture of ribonuclease P.
MeSH term(s)	Amino Acid Sequence ; Archaeal Proteins/chemistry ; Archaeoglobus fulgidus/enzymology ; Circular Dichroism ; Conserved Sequence ; Crystallization ; Crystallography, X-Ray ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Secondary ; Ribonuclease P/chemistry ; Ribonucleases/chemistry ; Ribonucleoproteins/chemistry ; Sequence Homology, Amino Acid ; Solutions
Chemical Substances	Archaeal Proteins ; Ribonucleoproteins ; Solutions ; Ribonucleases (EC 3.1.-) ; POP4 protein, human (EC 3.1.26.5) ; Ribonuclease P (EC 3.1.26.5)
Language	English
Publishing date	2004-11-09
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi048578z
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Article ; Online: Dual recruitment of Cdc48 (p97)-Ufd1-Npl4 ubiquitin-selective segregase by small ubiquitin-like modifier protein (SUMO) and ubiquitin in SUMO-targeted ubiquitin ligase-mediated genome stability functions.

Nie, Minghua / Aslanian, Aaron / Prudden, John / Heideker, Johanna / Vashisht, Ajay A / Wohlschlegel, James A / Yates, John R / Boddy, Michael N

The Journal of biological chemistry

2012 Volume 287, Issue 35, Page(s) 29610–29619

Abstract: Protein modification by SUMO and ubiquitin critically impacts genome stability via effectors that "read" their signals using SUMO interaction motifs or ubiquitin binding domains, respectively. A novel mixed SUMO and ubiquitin signal is generated by the ... ...

Abstract	Protein modification by SUMO and ubiquitin critically impacts genome stability via effectors that "read" their signals using SUMO interaction motifs or ubiquitin binding domains, respectively. A novel mixed SUMO and ubiquitin signal is generated by the SUMO-targeted ubiquitin ligase (STUbL), which ubiquitylates SUMO conjugates. Herein, we determine that the "ubiquitin-selective" segregase Cdc48-Ufd1-Npl4 also binds SUMO via a SUMO interaction motif in Ufd1 and can thus act as a selective receptor for STUbL targets. Indeed, we define key cooperative DNA repair functions for Cdc48-Ufd1-Npl4 and STUbL, thereby revealing a new signaling mechanism involving dual recruitment by SUMO and ubiquitin for Cdc48-Ufd1-Npl4 functions in maintaining genome stability.
MeSH term(s)	Adenosine Triphosphatases/genetics ; Adenosine Triphosphatases/metabolism ; Amino Acid Motifs ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; DNA Repair/physiology ; DNA, Fungal/genetics ; DNA, Fungal/metabolism ; Genomic Instability/physiology ; Protein Binding ; SUMO-1 Protein/genetics ; SUMO-1 Protein/metabolism ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; Signal Transduction/physiology ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination/physiology ; Valosin Containing Protein
Chemical Substances	Carrier Proteins ; Cell Cycle Proteins ; DNA, Fungal ; Npl4 protein, S pombe ; SUMO-1 Protein ; Schizosaccharomyces pombe Proteins ; Ubiquitin ; Ufd1 protein, S pombe ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Adenosine Triphosphatases (EC 3.6.1.-) ; Valosin Containing Protein (EC 3.6.4.6)
Language	English
Publishing date	2012-06-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M112.379768
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Article ; Online: DNA recognition by a σ(54) transcriptional activator from Aquifex aeolicus.

Vidangos, Natasha K / Heideker, Johanna / Lyubimov, Artem / Lamers, Meindert / Huo, Yixin / Pelton, Jeffrey G / Ton, Jimmy / Gralla, Jay / Berger, James / Wemmer, David E

Journal of molecular biology

2014 Volume 426, Issue 21, Page(s) 3553–3568

Abstract: Transcription initiation by bacterial σ(54)-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain (DBD). The structurally ... ...

Abstract	Transcription initiation by bacterial σ(54)-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain (DBD). The structurally characterized DBDs from activators all belong to the Fis (factor for inversion stimulation) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DBD of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of σ(54) activators. Two NtrC4-binding sites were identified upstream (-145 and -85bp) from the start of the lpxC gene, which is responsible for the first committed step in lipid A biosynthesis. This is the first experimental evidence for σ(54) regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145-binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homolog, Fis. The greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base-specific contacts contributing to affinity than for Fis.
MeSH term(s)	Bacteria/enzymology ; Bacterial Proteins/chemistry ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry ; Deoxyribonuclease I/chemistry ; Escherichia coli Proteins/chemistry ; Factor For Inversion Stimulation Protein/chemistry ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Nucleic Acid Conformation ; PII Nitrogen Regulatory Proteins/chemistry ; Protein Structure, Tertiary ; Proteins/chemistry ; RNA Polymerase Sigma 54/chemistry ; Transcription Factors/chemistry ; Transcription, Genetic ; Transcriptional Activation
Chemical Substances	Bacterial Proteins ; Escherichia coli Proteins ; Factor For Inversion Stimulation Protein ; PII Nitrogen Regulatory Proteins ; Proteins ; Transcription Factors ; glnG protein, E coli ; DNA (9007-49-2) ; RNA Polymerase Sigma 54 (EC 2.7.7.6) ; Deoxyribonuclease I (EC 3.1.21.1)
Language	English
Publishing date	2014-08-23
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2014.08.009
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Article ; Online: Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes

David S. Hewings / Johanna Heideker / Taylur P. Ma / Andrew P. AhYoung / Farid El Oualid / Alessia Amore / Gregory T. Costakes / Daniel Kirchhofer / Bradley Brasher / Thomas Pillow / Nataliya Popovych / Till Maurer / Carsten Schwerdtfeger / William F. Forrest / Kebing Yu / John Flygare / Matthew Bogyo / Ingrid E. Wertz

Nature Communications, Vol 9, Iss 1, Pp 1-

2018 Volume 17

Abstract: Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, ...

Abstract	Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases.
Keywords	Science ; Q
Language	English
Publishing date	2018-03-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
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Article ; Online: Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes

Nature Communications, Vol 9, Iss 1, Pp 1-

2018 Volume 17

Abstract	Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases.
Keywords	Science ; Q
Language	English
Publishing date	2018-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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