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

Echalier, Aude; Pan, Yunbao; Birol, Melissa; Tavernier, Nicolas; Pintard, Lionel; Hoh, François; Ebel, Christine; Galophe, Nathalie; Claret, François X.; Dumas, Christian

doi:10.1073/pnas.1209345110

Cited by 95 publications

(98 citation statements)

References 36 publications

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“…The active site of MPN domain metalloproteases is located between the N-terminal end of helix α3 and the adjacent β-strands βB and βD (31,33,34). Clear density for the catalytic zinc was identified between the sidechains of His109, His111, and Asp122 ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

Pathare

Nagy

Śledź

et al. 2014

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

120

131

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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...

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Section: Resultsmentioning

confidence: 99%

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

Pathare

Nagy

Śledź

et al. 2014

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

120

131

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“…The MPN-domain within CSN5 contains a metal chelating site and forms the catalytic region of the isopeptidase for deneddylation (27). Recently, the crystal structures of the CSN6-MPN domain and the CSN5 subunit have been revealed (28,29). Interestingly, amino acids 97-131, a flexible segment within the CSN5-MPN domain, were proven to be essential in regulating the isopeptidase states of CSN5 (29).…”

mentioning

confidence: 99%

“…Recently, the crystal structures of the CSN6-MPN domain and the CSN5 subunit have been revealed (28,29). Interestingly, amino acids 97-131, a flexible segment within the CSN5-MPN domain, were proven to be essential in regulating the isopeptidase states of CSN5 (29). PCI is an ∼200-amino acid domain, beginning with an N-terminal helical bundle arrangement and ending with a globular winged-helix subdomain (30,31).…”

mentioning

confidence: 99%

Crystal structure and versatile functional roles of the COP9 signalosome subunit 1

Lee

et al. 2013

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

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The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) plays key roles in many biological processes, such as repression of photomorphogenesis in plants and protein subcellular localization, DNA-damage response, and NF-κB activation in mammals. It is an evolutionarily conserved eight-protein complex with subunits CSN1 to CSN8 named following the descending order of molecular weights. Here, we report the crystal structure of the largest CSN subunit, CSN1 from Arabidopsis thaliana (atCSN1), which belongs to the Proteasome, COP9 signalosome, Initiation factor 3 (PCI) domain containing CSN subunit family, at 2.7 Å resolution. In contrast to previous predictions and distinct from the PCI-containing 26S proteasome regulatory particle subunit Rpn6 structure, the atCSN1 structure reveals an overall globular fold, with four domains consisting of helical repeat-I, linker helix, helical repeat-II, and the C-terminal PCI domain. Our small-angle X-ray scattering envelope of the CSN1-CSN7 complex agrees with the EM structure of the CSN alone (apo-CSN) and suggests that the PCI end of each molecule may mediate the interaction. Fitting of the CSN1 structure into the CSN-Skp1-Cul1-Fbox (SCF) EM structure shows that the PCI domain of CSN1 situates at the hub of the CSN for interaction with several other subunits whereas the linker helix and helical repeat-II of CSN1 contacts SCF using a conserved surface patch. Furthermore, we show that, in human, the C-terminal tail of CSN1, a segment not included in our crystal structure, interacts with IκBα in the NF-κB pathway. Therefore, the CSN complex uses multiple mechanisms to hinder NF-κB activation, a principle likely to hold true for its regulation of many other targets and pathways.T he constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a more than 300-kDa complex that was first identified as a negative regulator of Constitutive Photomorphogenesis (COP) in plants (1, 2). In the subsequent years, the highly conserved protein complex was also found in fungi (3, 4), Caenorhabditis elegans (5), Drosophila melanogaster (6), and mammals (7,8). The most studied function of the CSN complex in eukaryotes is the regulation of protein degradation through two pathways, deneddylation (9-11) and deubiquitination (12, 13). In the deneddylation pathway, the CSN complex can influence the cullin-RING ligase activity by removing Nedd8, a ubiquitin-like protein, from a cullin (9, 14). On the other hand, the CSN complex can also suppress cullin activity through recruitment of the deubiquitination enzyme USP15 (12) or Ubp12p, the Schizosaccharomyces pombe ortholog of human USP15 (13). Other functions of the CSN complex identified in mammalian cells include regulating the phosphorylation of ubiquitin-proteasome pathway substrates through CSN-associated kinases (7,(15)(16)(17)(18). Overall, the CSN complex appears to be a key player in protein subcellular localization (19,20), DNA-damage response (21), NF-κB activation (22), development, and cell cycle control (23,24). Thus, the functions ...

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“…AMSH-LP seems to be constitutively active, Rpn11 activity is promoted by rearrangements that bring the enzyme and its target substrate into proximity 13,14 , and CSN5 is activated by substrate-driven relief of inhibition. Strikingly, CSN5 is inhibited by distinct mechanisms depending on whether the subunit is on its own 15 or integrated into the CSN. Although some generalizations apply across the JAMM family, it is clear that each member has its own distinctive features.…”

Section: Corralling a Proteindegradation Regulatormentioning

confidence: 99%

Corralling a protein-degradation regulator

Deshaies

2014

Nature

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

Cited by 95 publications

References 36 publications

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

Crystal structure and versatile functional roles of the COP9 signalosome subunit 1

Corralling a protein-degradation regulator

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