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Article: Waste disposal in plants: where and how?

Kostova, Zlatka / Wolf, Dieter H

2003 Volume 8, Issue 10, Page(s) 461–462

MeSH term(s)	Endoplasmic Reticulum/physiology ; Medical Waste Disposal/methods ; Plant Physiological Phenomena ; Waste Disposal, Fluid/methods
Chemical Substances	Medical Waste Disposal
Language	English
Publishing date	2003-10
Publishing country	England
Document type	Journal Article
ZDB-ID	1305448-x
ISSN	1878-4372 ; 1360-1385
ISSN (online)	1878-4372
ISSN	1360-1385
DOI	10.1016/j.tplants.2003.08.004
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Article: Importance of carbohydrate positioning in the recognition of mutated CPY for ER-associated degradation.

Kostova, Zlatka / Wolf, Dieter H

Journal of cell science

2005 Volume 118, Issue Pt 7, Page(s) 1485–1492

Abstract: In the endoplasmic reticulum (ER), N-linked glycans (N-glycans) function as signals to recruit the lectin chaperones involved in protein folding, quality control and ER-associated degradation. We undertook a systematic study of the four N-glycans of ... ...

Abstract	In the endoplasmic reticulum (ER), N-linked glycans (N-glycans) function as signals to recruit the lectin chaperones involved in protein folding, quality control and ER-associated degradation. We undertook a systematic study of the four N-glycans of mutated carboxypeptidase yscY (CPY) to determine whether there are positional differences between the glycans in ER-associated degradation. We constructed hypoglycosylated CPY variants containing one, two or three N-glycans in various combinations and studied their degradation kinetics. We found that the four carbohydrate chains on CPY* are not equal in their signaling function: presence of the Asn368-linked glycan is necessary and sufficient for efficient degradation of CPY*. We also analysed the involvement of the ER lectins Htm1p and Cne1p (yeast calnexin) in the glycan-based recognition process with respect to number and position of N-glycans. We observed that Htm1p function depends on the presence of N-glycans in general but that there is no positional preference for a particular glycan. Cne1p, however, is selective with respect to substrate, and participates in the quality control only of some underglycosylated variants. For cases in which both lectins are involved, Cne1p and Htm1p play competing roles in targeting the substrate for degradation: loss of Cne1p accelerates degradation, whereas loss of Htm1p stabilizes the substrate.
MeSH term(s)	Amino Acid Sequence ; Calnexin ; Carbohydrate Metabolism ; Carbohydrates/chemistry ; Carbohydrates/genetics ; Carboxypeptidases/chemistry ; Carboxypeptidases/genetics ; Carboxypeptidases/metabolism ; Endoplasmic Reticulum/metabolism ; Glycosylation ; Kinetics ; Lectins/metabolism ; Mannosidases/metabolism ; Membrane Proteins/metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Polysaccharides/chemistry ; Polysaccharides/physiology ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction/physiology ; Time Factors
Chemical Substances	CNE1 protein, S cerevisiae ; Carbohydrates ; Lectins ; Membrane Proteins ; Polysaccharides ; Saccharomyces cerevisiae Proteins ; Calnexin (139873-08-8) ; MNL1 protein, S cerevisiae (EC 3.2.1.-) ; Mannosidases (EC 3.2.1.-) ; Carboxypeptidases (EC 3.4.-) ; serine carboxypeptidase (EC 3.4.16.5)
Language	English
Publishing date	2005-04-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.01740
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Article: For whom the bell tolls: protein quality control of the endoplasmic reticulum and the ubiquitin-proteasome connection.

Kostova, Zlatka / Wolf, Dieter H

The EMBO journal

2003 Volume 22, Issue 10, Page(s) 2309–2317

Abstract: The surveillance of the structural fidelity of the proteome is of utmost importance to all cells. The endoplasmic reticulum (ER) is the organelle responsible for proper folding and delivery of proteins to the secretory pathway. It contains a ... ...

Abstract	The surveillance of the structural fidelity of the proteome is of utmost importance to all cells. The endoplasmic reticulum (ER) is the organelle responsible for proper folding and delivery of proteins to the secretory pathway. It contains a sophisticated protein proofreading and elimination mechanism. Failure of this machinery leads to disease and, finally, to cell death. Elimination of misfolded proteins requires retrograde transport across the ER membrane and depends on the central cytoplasmic proteolytic machinery involved in cellular regulation: the ubiquitin-proteasome system. The basics of this process as well as recent advances in the field are reviewed.
MeSH term(s)	Endoplasmic Reticulum/metabolism ; Fungal Proteins/metabolism ; Models, Biological ; Peptide Hydrolases/metabolism ; Proteasome Endopeptidase Complex ; Protein Folding ; Protein Transport/physiology ; Ubiquitin/metabolism
Chemical Substances	Fungal Proteins ; Ubiquitin ; Peptide Hydrolases (EC 3.4.-) ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; ATP dependent 26S protease (EC 3.4.99.-)
Language	English
Publishing date	2003-05-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.1093/emboj/cdg227
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Article: Ubiquitin ligases, critical mediators of endoplasmic reticulum-associated degradation.

Kostova, Zlatka / Tsai, Yien Che / Weissman, Allan M

Seminars in cell & developmental biology

2007 Volume 18, Issue 6, Page(s) 770–779

Abstract: Endoplasmic reticulum-associated degradation (ERAD) represents the primary means of quality control within the secretory pathway. Critical to this process are ubiquitin protein ligases (E3s) which, together with ubiquitin conjugating enzymes (E2s), ... ...

Abstract	Endoplasmic reticulum-associated degradation (ERAD) represents the primary means of quality control within the secretory pathway. Critical to this process are ubiquitin protein ligases (E3s) which, together with ubiquitin conjugating enzymes (E2s), mediate the ubiquitylation of proteins targeted for degradation from the ER. In this chapter we review our knowledge of both Saccharomyces cerevisiae and mammalian ERAD ubiquitin ligases. We focus on recent insights into these E3s, their associated proteins and potential mechanisms of action.
MeSH term(s)	Animals ; Endoplasmic Reticulum/metabolism ; Humans ; Mammals ; Proteins/metabolism ; Saccharomyces cerevisiae Proteins ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
Chemical Substances	Proteins ; Saccharomyces cerevisiae Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2007-09-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2007.09.002
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Article: Importance of carbohydrate positioning in the recognition of mutated CPY for ER-associated degradation

Kostova, Zlatka / Wolf, Dieter H

Journal of cell science. 2005 Apr. 1, v. 118, no. 7

2005

Abstract	In the endoplasmic reticulum (ER), N-linked glycans (N-glycans) function as signals to recruit the lectin chaperones involved in protein folding, quality control and ER-associated degradation. We undertook a systematic study of the four N-glycans of mutated carboxypeptidase yscY (CPY) to determine whether there are positional differences between the glycans in ER-associated degradation. We constructed hypoglycosylated CPY variants containing one, two or three N-glycans in various combinations and studied their degradation kinetics. We found that the four carbohydrate chains on CPY* are not equal in their signaling function: presence of the Asn368-linked glycan is necessary and sufficient for efficient degradation of CPY*. We also analysed the involvement of the ER lectins Htm1p and Cne1p (yeast calnexin) in the glycan-based recognition process with respect to number and position of N-glycans. We observed that Htm1p function depends on the presence of N-glycans in general but that there is no positional preference for a particular glycan. Cne1p, however, is selective with respect to substrate, and participates in the quality control only of some underglycosylated variants. For cases in which both lectins are involved, Cne1p and Htm1p play competing roles in targeting the substrate for degradation: loss of Cne1p accelerates degradation, whereas loss of Htm1p stabilizes the substrate.
Language	English
Dates of publication	2005-0401
Size	p. 1485-1492.
Document type	Article
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
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Article: A Ubc7p-binding domain in Cue1p activates ER-associated protein degradation

Kostova, Zlatka / Mariano, Jennifer / Scholz, Simone / Koenig, Carolin / Weissman, Allan M

Journal of cell science. 2009 May 1, v. 122, no. 9

2009

Abstract: Cue1p is an N-terminally anchored endoplasmic reticulum (ER) protein essential for the activity of the two major yeast RING finger ubiquitin ligases (E3s) implicated in ER-associated degradation (ERAD). Cue1p contains a CUE domain, which for several ... ...

Abstract	Cue1p is an N-terminally anchored endoplasmic reticulum (ER) protein essential for the activity of the two major yeast RING finger ubiquitin ligases (E3s) implicated in ER-associated degradation (ERAD). Cue1p contains a CUE domain, which for several proteins is known to bind ubiquitin. We now establish that the CUE domain is dispensable for ERAD of substrates of both Hrd1p and Doa10p and that the Cue1p transmembrane domain is similarly not required for degradation of the Hrd1p substrate CPY*. Cue1p interacts with the ERAD E2 Ubc7p in vivo. We show that a discrete C-terminal Ubc7p binding region (U7BR) of Cue1p is required for ERAD and for Ubc7p-dependent ubiquitylation by Hrd1p in vitro. Strikingly, when Ubc7p is stabilized by direct anchoring to the ER membrane, the U7BR is sufficient to restore ERAD in cells lacking Cue1p. Thus, discrete E2 binding sites independent of ubiquitin ligase domains have the potential to activate ubiquitylation.
Language	English
Dates of publication	2009-0501
Size	p. 1374-1381.
Publishing place	The Company of Biologists Limited
Document type	Article
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
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Article: A Ubc7p-binding domain in Cue1p activates ER-associated protein degradation.

Kostova, Zlatka / Mariano, Jennifer / Scholz, Simone / Koenig, Carolin / Weissman, Allan M

Journal of cell science

2009 Volume 122, Issue Pt 9, Page(s) 1374–1381

Abstract	Cue1p is an N-terminally anchored endoplasmic reticulum (ER) protein essential for the activity of the two major yeast RING finger ubiquitin ligases (E3s) implicated in ER-associated degradation (ERAD). Cue1p contains a CUE domain, which for several proteins is known to bind ubiquitin. We now establish that the CUE domain is dispensable for ERAD of substrates of both Hrd1p and Doa10p and that the Cue1p transmembrane domain is similarly not required for degradation of the Hrd1p substrate CPY. Cue1p interacts with the ERAD E2 Ubc7p in vivo. We show that a discrete C-terminal Ubc7p binding region (U7BR) of Cue1p is required for ERAD and for Ubc7p-dependent ubiquitylation by Hrd1p in vitro. Strikingly, when Ubc7p is stabilized by direct anchoring to the ER membrane, the U7BR is sufficient to restore ERAD in cells lacking Cue1p. Thus, discrete E2 binding sites independent of ubiquitin ligase domains have the potential to activate ubiquitylation.
MeSH term(s)	Animals ; Carrier Proteins/chemistry ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Endoplasmic Reticulum/metabolism ; Endoplasmic Reticulum/ultrastructure ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Models, Molecular ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Ubiquitin-Conjugating Enzymes/genetics ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
Chemical Substances	CUE1 protein, S cerevisiae ; Carrier Proteins ; Membrane Proteins ; Recombinant Fusion Proteins ; Saccharomyces cerevisiae Proteins ; UBC7 protein, S cerevisiae (EC 2.3.2.23) ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23) ; HRD1 protein, S cerevisiae (EC 2.3.2.27) ; SSM4 protein, S cerevisiae (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2009-04-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.044255
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Article: A genome-wide screen identifies Yos9p as essential for ER-associated degradation of glycoproteins.

Buschhorn, Bettina A / Kostova, Zlatka / Medicherla, Balasubrahmanyam / Wolf, Dieter H

FEBS letters

2004 Volume 577, Issue 3, Page(s) 422–426

Abstract: We undertook a growth-based screen exploiting the degradation of CTL*, a chimeric membrane-bound ERAD substrate derived from soluble lumenal CPY*. We screened the Saccharomyces cerevisiae genomic deletion library containing approximately 5000 viable ... ...

Abstract	We undertook a growth-based screen exploiting the degradation of CTL, a chimeric membrane-bound ERAD substrate derived from soluble lumenal CPY. We screened the Saccharomyces cerevisiae genomic deletion library containing approximately 5000 viable strains for mutants defective in endoplasmic reticulum (ER) protein quality control and degradation (ERAD). Among the new gene products we identified Yos9p, an ER-localized protein previously involved in the processing of GPI anchored proteins. We show that deficiency in Yos9p affects the degradation only of glycosylated ERAD substrates. Degradation of non-glycosylated substrates is not affected in cells lacking Yos9p. We propose that Yos9p is a lectin or lectin-like protein involved in the quality control of N-glycosylated proteins. It may act sequentially or in concert with the ERAD lectin Htm1p/Mnl1p (EDEM) to prevent secretion of malfolded glycosylated proteins and deliver them to the cytosolic ubiquitin-proteasome machinery for elimination.
MeSH term(s)	Carrier Proteins/chemistry ; Carrier Proteins/metabolism ; Cell Membrane/metabolism ; Endoplasmic Reticulum/metabolism ; Gene Deletion ; Genetic Complementation Test ; Glycoproteins/genetics ; Glycoproteins/metabolism ; Kinetics ; Methionine/metabolism ; Models, Biological ; Plasmids/metabolism ; Precipitin Tests ; Protein Structure, Tertiary ; Quality Control ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/growth & development ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Substrate Specificity ; Sulfur Radioisotopes ; Temperature
Chemical Substances	Carrier Proteins ; Glycoproteins ; Saccharomyces cerevisiae Proteins ; Sulfur Radioisotopes ; Yos9 protein, S cerevisiae ; Methionine (AE28F7PNPL)
Language	English
Publishing date	2004-11-19
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2004.10.039
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Article: A genomic screen identifies Dsk2p and Rad23p as essential components of ER-associated degradation.

Medicherla, Balasubrahmanyam / Kostova, Zlatka / Schaefer, Antje / Wolf, Dieter H

EMBO reports

2004 Volume 5, Issue 7, Page(s) 692–697

Abstract: We developed a growth test to screen for yeast mutants defective in endoplasmic reticulum (ER) quality control and associated protein degradation (ERAD) using the membrane protein CTL*, a chimeric derivative of the classical ER degradation substrate CPY*. ...

Abstract	We developed a growth test to screen for yeast mutants defective in endoplasmic reticulum (ER) quality control and associated protein degradation (ERAD) using the membrane protein CTL, a chimeric derivative of the classical ER degradation substrate CPY. In a genomic screen of approximately 5,000 viable yeast deletion mutants, we identified genes necessary for ER quality control and degradation. Among the new gene products, we identified Dsk2p and Rad23p. We show that these two proteins are probably delivery factors for ubiquitinated ER substrates to the proteasome, following their removal from the membrane via the Cdc48-Ufd1-Npl4p complex. In contrast to the ERAD substrate CTG, proteasomal degradation of a cytosolic CPY-GFP fusion is not dependent on Dsk2p and Rad23p, indicating pathway specificity for both proteins. We propose that, in certain degradation pathways, Dsk2p, Rad23p and the trimeric Cdc48 complex function together in the delivery of ubiquitinated proteins to the proteasome, avoiding malfolded protein aggregates in the cytoplasm.
MeSH term(s)	Adenosine Triphosphatases ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Cell Cycle Proteins/physiology ; Cell Membrane/metabolism ; Cycloheximide/pharmacology ; Cytoplasm/metabolism ; Cytosol/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/physiology ; Endoplasmic Reticulum/metabolism ; Gene Deletion ; Genetic Techniques ; Genome, Fungal ; Green Fluorescent Proteins/metabolism ; Immunoprecipitation ; Models, Chemical ; Mutation ; Nuclear Pore Complex Proteins/metabolism ; Nucleocytoplasmic Transport Proteins ; Open Reading Frames ; Proteasome Endopeptidase Complex/metabolism ; Protein Folding ; Protein Synthesis Inhibitors/pharmacology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/physiology ; Time Factors ; Ubiquitin/metabolism ; Ubiquitins/genetics ; Ubiquitins/physiology ; Valosin Containing Protein ; Vesicular Transport Proteins
Chemical Substances	Cell Cycle Proteins ; DNA-Binding Proteins ; DSK2 protein, S cerevisiae ; NPL4 protein, S cerevisiae ; Nuclear Pore Complex Proteins ; Nucleocytoplasmic Transport Proteins ; Protein Synthesis Inhibitors ; RAD23 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; UFD1 protein, S cerevisiae ; Ubiquitin ; Ubiquitins ; Vesicular Transport Proteins ; Green Fluorescent Proteins (147336-22-9) ; Cycloheximide (98600C0908) ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Adenosine Triphosphatases (EC 3.6.1.-) ; CDC48 protein, S cerevisiae (EC 3.6.4.-) ; Valosin Containing Protein (EC 3.6.4.6)
Language	English
Publishing date	2004-05-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.1038/sj.embor.7400164
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Article ; Online: A structurally unique E2-binding domain activates ubiquitination by the ERAD E2, Ubc7p, through multiple mechanisms.

Metzger, Meredith B / Liang, Yu-He / Das, Ranabir / Mariano, Jennifer / Li, Shengjian / Li, Jess / Kostova, Zlatka / Byrd, R Andrew / Ji, Xinhua / Weissman, Allan M

Molecular cell

2013 Volume 50, Issue 4, Page(s) 516–527

Abstract: Cue1p is an integral component of yeast endoplasmic reticulum (ER)-associated degradation (ERAD) ubiquitin ligase (E3) complexes. It tethers the ERAD ubiquitin-conjugating enzyme (E2), Ubc7p, to the ER and prevents its degradation, and also activates ... ...

Abstract	Cue1p is an integral component of yeast endoplasmic reticulum (ER)-associated degradation (ERAD) ubiquitin ligase (E3) complexes. It tethers the ERAD ubiquitin-conjugating enzyme (E2), Ubc7p, to the ER and prevents its degradation, and also activates Ubc7p via unknown mechanisms. We have now determined the crystal structure of the Ubc7p-binding region (U7BR) of Cue1p with Ubc7p. The U7BR is a unique E2-binding domain that includes three α-helices that interact extensively with the "backside" of Ubc7p. Residues essential for E2 binding are also required for activation of Ubc7p and for ERAD. We establish that the U7BR stimulates both RING-independent and RING-dependent ubiquitin transfer from Ubc7p. Moreover, the U7BR enhances ubiquitin-activating enzyme (E1)-mediated charging of Ubc7p with ubiquitin. This demonstrates that an essential component of E3 complexes can simultaneously bind to E2 and enhance its loading with ubiquitin. These findings provide mechanistic insights into how ubiquitination can be stimulated.
MeSH term(s)	Amino Acid Sequence ; Binding Sites/genetics ; Carrier Proteins/chemistry ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Crystallography, X-Ray ; Electrophoresis, Polyacrylamide Gel ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Binding ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Homology, Amino Acid ; Static Electricity ; Substrate Specificity ; Ubiquitin-Conjugating Enzymes/chemistry ; Ubiquitin-Conjugating Enzymes/genetics ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitination
Chemical Substances	CUE1 protein, S cerevisiae ; Carrier Proteins ; Membrane Proteins ; Saccharomyces cerevisiae Proteins ; UBC7 protein, S cerevisiae (EC 2.3.2.23) ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23)
Language	English
Publishing date	2013-05-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2013.04.004
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