Structural analysis of recombinant human ubiquitin-conjugating enzyme UbcH5c

Wu, Fangshu; Zhu, Jia‐Ying; Li, Honglin; Zhu, Lili

doi:10.1016/j.apsb.2016.12.008

Cited by 9 publications

(10 citation statements)

References 20 publications

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“…IDD is predominantly characterized by the imbalance of extracellular matrix synthesis and degradation, as well as increased apoptosis and senescence in nucleus pulposus (NP) cells 6 – 9 . As reported, proinflammatory cytokines, such as IL-1β, IL-1α, TNF-α, and IL-6 were increased in degenerative intervertebral disc.…”

Section: Introductionmentioning

confidence: 99%

Parkin-mediated mitophagy as a potential therapeutic target for intervertebral disc degeneration

Zhang

Chen

et al. 2018

Cell Death Dis

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Intervertebral disc degeneration (IDD) is a complicated pathological condition blamed for low back pain. Mitochondrion is of vital importance for cellular homeostasis, and mitochondrial dysfunction is considered to be one of the major causes of cellular damage. Mitophagy is a cellular process to eliminate impaired mitochondria and showed protective effects in various diseases; however, its role in IDD is still not clear. Here, we explore the role of Parkin-mediated mitophagy in IDD. In this study, we found that Parkin was upregulated in degenerative nucleus pulposus (NP) tissues in vivo as well as in TNF-α stimulated NP cells in vitro. Knockdown of Parkin by siRNA showed that Parkin is crucial for apoptosis and mitochondrion homeostasis in NP cells. Further study showed that upregulation of Parkin by salidroside may eliminate impaired mitochondria and promote the survival of NP cells through activation of mitophagy in vitro. In in vivo study, we found that salidroside could inhibit the apoptosis of NP cells and ameliorate the progression of IDD. These results suggested that Parkin is involved in the pathogenesis of IDD and may be a potential therapeutic target for IDD.

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Section: Introductionmentioning

confidence: 99%

Parkin-mediated mitophagy as a potential therapeutic target for intervertebral disc degeneration

Zhang

Chen

et al. 2018

Cell Death Dis

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“…Sequence alignment and structure superposition analysis. Human UbcH5s (UbcH5a 24 , UbcH5b 25 and UbcH5c 26 ) sequence alignment and structural superposition were performed using CLUSTALW 27 , ESPript 3.0 28 and PyMol 1.6 29 (as shown in Fig. 2A,B).…”

Section: Resultsmentioning

confidence: 99%

Molecular Simulation Elaborating the Mechanism of 1β-Hydroxy Alantolactone Inhibiting Ubiquitin-Conjugating Enzyme UbcH5s

Meng

2020

Sci Rep

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1β-hydroxy alantolactone, a sesquiterpene lactone, exhibits potent anti-inflammatory and anticancer activities. Recently, it has been found to target UbcH5s by covalently bonding with Cys85 specifically, but the exact molecular basis remains unclear. Here, we analyzed the structural specificity of the catalytic site of UbcH5s by comparing them with other E2 proteins. Molecular dynamics was performed to detect the structural stability of the catalytic site. Docking method was then used to predict conformations of ligand docked at the catalytic site of UbcH5s. The electrostatic surface and charge distribution of ligand and proteins were analyzed by quantitative calculation. Molecular dynamics was used to detect the stability of docking complexes of 1β-hydroxy alantolactone and UbcH5s, the covalently bonded intermediates and the products. The QM/MM methodology was used to calculate the free energy barrier of hydrogen transfer and formation of covalent bond between 15-position carbon of ligand and Cys85. Results revealed that the structure of the catalytic site is stable, and 1β-hydroxy alantolactone can dock at the catalytic site with correct conformation. Molecular dynamics further demonstrates that 1β-hydroxy alantolactone can steadily combine with UbcH5s. Intermediate and product of catalytic reaction are also certified to be stable. Besides, Asp112 and Asn114 function as anchors to fix ligand, ensuring it steadily docked at catalytic site to complete covalent reaction. More importantly, we have found that Cys85 of UbcH5c is more efficient to form a covalent bond with the ligand in comparison with UbcH5a and UbcH5b. Our results successfully explained the mechanism of 1β-hydroxy alantolactone covalently bonding with UbcH5s. Such molecular mechanism may provide a better insight into the molecular development or modification for ubiquitin-related drugs. Recent studies have indicated that medicinal herbs have been gradually widely used despite insufficient information correlating with their mechanism of action. At present, research institutions or companies are devoting themselves to discovery a class of bioactive compounds, their valuable target proteins and mechanisms of action against diseases. Sesquiterpene lactones are plant-derived bioactive constituents, which have subjected numerous studies. Researches revealed that they could be used in medicines against inflammation, cancer, malaria, and viral and bacterial infection 1,2. Pharmacodynamic studies further reported that sesquiterpene lactones might exert therapeutic effects by inhibiting NF-κB and MAPK pathway activation 3-8. Nevertheless, the molecular mechanism of sesquiterpene lactones targeting protein on NF-κB and MAPK pathway is unknown. 1β-hydroxy alantolactone that belonged to sesquiterpene lactone has been found to possess anti-inflammatory and anticancer activities. From the data of its discovery, studies reported almost the same pharmacological effects of 1β-hydroxy alantolactone and its derivatives 9 , of which they can covalently bond with Cys38 o...

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“…(a) Ribbon representation of UBE2D2 (PDB: 2ESK), showing the residues involved in catalysis as ball‐and‐sticks, and highlighting the E1‐/E3‐binding sites. The ribbon diagram is colored to reflect the average pairwise positional shift of each overlapping C α atom between UBE2D2 and UBE2A (PDB: 6CYO), UBE2B (PDB: 1JAS), UBE2C (PDB: 1I7K), UBE2D1 (PDB: 2C4P), UBE2D3 (PDB: 5EGG), UBE2E1 (PDB: 5BZH), UBE2E2 (PDB: 1Y6I), UBE2G1 (PDB: 2AWF), UBE2H (PDB: 2Z5D), UBE2J2 (PDB: 2F4W), UBE2K (PDB: 1YLA), UBE2Q1 (PDB: 2QGX), UBE2Q2 (PDB: 1ZUO), UBE2R1 (PDB: 2OB4), UBE2S (PDB: 1ZDN), UBE2T (PDB: 1YH2), UBE2U (PDB: 1YRV), UBE2V1 (PDB: 2A4D), BIRC6 (PDB: 3CEG), UBE2F (PDB: 2EDI), UBE2G2 (PDB: 2CYX), UBE2I (PDB: 1A3S), UBE2L3 (PDB: 5TTE), UBE2L6: (PDB: 1WZW), UBE2M (PDB: 1Y8X), UBE2N (PDB: 2C2V), UBE2V2 (PDB: 4ONM), UBE2W (PDB: 2MT6), and UBE2Z (PDB: 5A4P) . (b) UBE2D2, UBE2N, UBE2L3, and UBE2T E3‐binding sites, made up of their respective helix 1 (α1), Loop 4 (L4), and Loop 7 (L7), shown as surface representation, with the surface colored using the “Yellow‐Red‐Blue” script, which colors surface‐exposed hydrophobic, negatively charged and positively charged residues yellow, red, and blue, respectively.…”

Section: E2 Morphologymentioning

confidence: 99%

Structural basis of generic versus specific E2–RING E3 interactions in protein ubiquitination

Gundogdu

Walden

2019

Protein Science

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Protein ubiquitination is a fundamental regulatory component in eukaryotic cell biology, where a cascade of ubiquitin activating (E1), conjugating (E2), and ligating (E3) enzymes assemble distinct ubiquitin signals on target proteins. E2s specify the type of ubiquitin signal generated, while E3s associate with the E2~Ub conjugate and select the substrate for ubiquitination. Thus, producing the right ubiquitin signal on the right target requires the right E2–E3 pair. The question of how over 600 E3s evolved to discriminate between 38 structurally related E2s has therefore been an area of intensive research, and with over 50 E2–E3 complex structures generated to date, the answer is beginning to emerge. The following review discusses the structural basis of generic E2–RING E3 interactions, contrasted with emerging themes that reveal how specificity can be achieved.

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Structural analysis of recombinant human ubiquitin-conjugating enzyme UbcH5c

Cited by 9 publications

References 20 publications

Parkin-mediated mitophagy as a potential therapeutic target for intervertebral disc degeneration

Parkin-mediated mitophagy as a potential therapeutic target for intervertebral disc degeneration

Molecular Simulation Elaborating the Mechanism of 1β-Hydroxy Alantolactone Inhibiting Ubiquitin-Conjugating Enzyme UbcH5s

Structural basis of generic versus specific E2–RING E3 interactions in protein ubiquitination

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