The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6

Zhang, Heng; Gao, Zengqiang; Wang, Wenjia; Liu, Guangfeng; Shtykova, Eleonora V.; Xu, Jianhua; Li, Lanfen; Su, Xiao‐Dong; Dong, Yuhan

doi:10.1016/j.febslet.2012.03.029

Cited by 21 publications

(22 citation statements)

References 30 publications

(73 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, the carboxyl group of Asp142 links the amide groups of Gly115 and Ile144. These two interactions are conserved in Csn5 as well (31,32) (Fig. S4F).…”

Section: Resultsmentioning

confidence: 94%

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

Pathare

Nagy

Śledź

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

120

131

View full text Add to dashboard Cite

The ATP-dependent degradation of polyubiquitylated proteins by the 26S proteasome is essential for the maintenance of proteome stability and the regulation of a plethora of cellular processes. Degradation of substrates is preceded by the removal of polyubiquitin moieties through the isopeptidase activity of the subunit Rpn11. Here we describe three crystal structures of the heterodimer of the Mpr1-Pad1-N-terminal domains of Rpn8 and Rpn11, crystallized as a fusion protein in complex with a nanobody. This fusion protein exhibits modest deubiquitylation activity toward a model substrate. Full activation requires incorporation of Rpn11 into the 26S proteasome and is dependent on ATP hydrolysis, suggesting that substrate processing and polyubiquitin removal are coupled. Based on our structures, we propose that premature activation is prevented by the combined effects of low intrinsic ubiquitin affinity, an insertion segment acting as a physical barrier across the substrate access channel, and a conformationally unstable catalytic loop in Rpn11. The docking of the structure into the proteasome EM density revealed contacts of Rpn11 with ATPase subunits, which likely stabilize the active conformation and boost the affinity for the proximal ubiquitin moiety. The narrow space around the Rpn11 active site at the entrance to the ATPase ring pore is likely to prevent erroneous deubiquitylation of folded proteins.n eukaryotes, the ubiquitin (Ub) proteasome system (UPS) is responsible for the regulated degradation of proteins (1-5). The UPS plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer needed. Consequently, the UPS is critically involved in numerous cellular processes, including cell cycle progression, apoptosis, and DNA damage repair, and malfunctions of the system often result in disease.The 26S proteasome executes the degradation of substrates that are marked for destruction by the covalent attachment of polyubiquitin chains. It is a molecular machine of 2.5 MDa comprising two subcomplexes, the 20S core particle (CP) and one or two 19S regulatory particles (RPs), which associate with the ends of the cylinder-shaped CP (6-8). The recognition and recruitment of polyubiquitylated substrates, their deubiquitylation, ATP-dependent unfolding, and translocation into the core particle take place in the RP. The structurally and mechanistically well-characterized CP houses the proteolytic activities and sequesters them from the environment, thereby avoiding collateral damage (9).The RPs attach to the outer α-rings of the CP, which control access to the proteolytic chamber formed by the inner β-subunit rings (10). Recently, the molecular architecture of the 26S holocomplex was established using cryo-EM-based approaches (11,12), and a pseudoatomic model of the holocomplex was put forward (13). The RP is formed by two subcomplexes, known as the base and the lid, which assemble independent...

show abstract

“…In addition, the carboxyl group of Asp142 links the amide groups of Gly115 and Ile144. These two interactions are conserved in Csn5 as well (31,32) (Fig. S4F).…”

Section: Resultsmentioning

confidence: 94%

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

Pathare

Nagy

Śledź

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

120

131

View full text Add to dashboard Cite

show abstract

“…Supported by both in vitro and in vivo data, these observations suggest that a CSN5 dimeric assembly could be present in solution in equilibrium with monomeric species (SI Appendix, Tables S3 and S4). It is noteworthy that other MPN-containing proteins were found to assemble in dimers in the crystals and that each of the described dimers proceeds via totally different interfaces (16,17), preventing further comparison. Moreover, the question of the physiological relevance of these dimers has not yet been addressed in vivo.…”

Section: Resultsmentioning

confidence: 98%

Insights into the regulation of the human COP9 signalosome catalytic subunit, CSN5/Jab1

Echalier

Pan

Birol

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The COP9 (Constitutive photomorphogenesis 9) signalosome (CSN), a large multiprotein complex that resembles the 19S lid of the 26S proteasome, plays a central role in the regulation of the E3-cullin RING ubiquitin ligases (CRLs). The catalytic activity of the CSN complex, carried by subunit 5 (CSN5/Jab1), resides in the deneddylation of the CRLs that is the hydrolysis of the cullin-neural precursor cell expressed developmentally downregulated gene 8 (Nedd8)isopeptide bond. Whereas CSN-dependent CSN5 displays isopeptidase activity, it is intrinsically inactive in other physiologically relevant forms. Here we analyze the crystal structure of CSN5 in its catalytically inactive form to illuminate the molecular basis for its activation state. We show that CSN5 presents a catalytic domain that brings essential elements to understand its activity control. Although the CSN5 active site is catalytically competent and compatible with di-isopeptide binding, the Ins-1 segment obstructs access to its substrate-binding site, and structural rearrangements are necessary for the Nedd8-binding pocket formation. Detailed study of CSN5 by molecular dynamics unveils signs of flexibility and plasticity of the Ins-1 segment. These analyses led to the identification of a molecular trigger implicated in the active/inactive switch that is sufficient to impose on CSN5 an active isopeptidase state. We show that a single mutation in the Ins-1 segment restores biologically relevant deneddylase activity. This study presents detailed insights into CSN5 regulation. Additionally, a dynamic monomer-dimer equilibrium exists both in vitro and in vivo and may be functionally relevant.C ell signaling processes mediated by ubiquitinylation, the posttranslational covalent conjugation of ubiquitin molecules, are of prime importance for cellular activity and particularly for protein turnover. Ubiquitin-ligase enzymes (E3s) are responsible for the last step of the ubiquitinylation reaction, and the multisubunit cullin-RING E3 ubiquitin ligases (CRLs) represent the most prominent of E3 enzymes. Among the several factors that regulate CRL activity, cullin neddylation/deneddylation cycles are central (1).The Cop9 signalosome (CSN), which is an eight-subunit complex largely conserved through evolution, deneddylates CRLs and thereby regulates CRL activity. As a large number of proteins are ubiquitinylated by CRLs, the CSN complex is implicated in the control of a significant proportion of the proteome, including prooncogenes, tumor suppressors, and other important cellular protagonists (1). Not surprisingly, the CSN has been implicated in various cellular functions, ranging from cell cycles to circadian rhythm and to immunity in various organisms. Furthermore, many studies have found a strong link between the CSN and cancers (2).The CSN, a multi-protein complex of about 320 kDa, contains six proteasome Cop9 eIF3 (PCI)-based subunits and two MPR1-Pad1-N-terminal (MPN)-based subunits. The subunit 5 [CSN5; also known as c-Jun activation domain-binding protein-1 (...

show abstract

“…The PCR products were digested and then cloned into the pET28at-plus vector (11), introducing an N-terminal His tag followed by a tobacco etch virus cleavage site. These expression plasmids were transformed into Escherichia coli strain BL21 (DE3).…”

Section: Methodsmentioning

confidence: 99%

Structure of the Type VI Effector-Immunity Complex (Tae4-Tai4) Provides Novel Insights into the Inhibition Mechanism of the Effector by Its Immunity Protein*

Zhang

Gao

Wang

et al. 2013

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Background:The bacteria effector Tae4 is injected into the recipient cells to kill them and the immunity protein Tai4 is produced to inactivate Tae4. Results: Tae4 displays a papain-like fold, and Tai4 dimer is responsible for inhibiting Tae4 activity. Conclusion:The inactivation of Tae4 is required by collaboration of both subunits of Tai4 dimer. Significance: Our results add new insights into the effector-immunity interaction module.

show abstract

The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6

Cited by 21 publications

References 30 publications

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

Insights into the regulation of the human COP9 signalosome catalytic subunit, CSN5/Jab1

Structure of the Type VI Effector-Immunity Complex (Tae4-Tai4) Provides Novel Insights into the Inhibition Mechanism of the Effector by Its Immunity Protein*

Contact Info

Product

Resources

About