Page last updated: 2024-10-24

regulation of protein neddylation

Definition

Target type: biologicalprocess

Any process that modulates the frequency, rate or extent of protein neddylation. [GOC:obol]

Protein neddylation, a ubiquitin-like modification, is a crucial regulatory mechanism in various cellular processes. The process involves the covalent attachment of the ubiquitin-like protein NEDD8 (Neural precursor cell expressed, developmentally downregulated 8) to a lysine residue on target proteins, primarily cullin-RING ligases (CRLs).

NEDD8 conjugation proceeds through a series of enzymatic steps, similar to ubiquitination.

1. **Activation:** NEDD8 is first activated by the E1 enzyme, NEDD8-activating enzyme (NAE), which utilizes ATP to form a thioester bond between NEDD8 and the E1 enzyme.

2. **Conjugation:** The activated NEDD8 is then transferred to the E2 enzyme, NEDD8-conjugating enzyme (UBE2F), forming a NEDD8-E2 thioester intermediate.

3. **Ligation:** Finally, the E3 ligase, a cullin-RING ligase (CRL), facilitates the transfer of NEDD8 from the E2 to a lysine residue on a target protein, typically a cullin subunit within the CRL.

NEDD8 conjugation to CRLs is essential for their activity. CRLs function as E3 ubiquitin ligases, responsible for targeting specific proteins for ubiquitination and subsequent degradation by the proteasome. NEDD8 modification of cullins enhances their catalytic activity, thereby regulating the ubiquitination and degradation of numerous cellular substrates.

The regulation of protein neddylation plays a critical role in a wide range of cellular processes, including:

* **Cell cycle control:** Neddylation regulates the activity of key cell cycle proteins, such as cyclin-dependent kinases (CDKs) and anaphase promoting complex (APC).
* **DNA damage response:** Neddylation influences the activation and function of DNA repair pathways.
* **Signal transduction:** Neddylation modulates signaling pathways, including the NF-κB and Wnt pathways.
* **Immune response:** Neddylation contributes to the regulation of immune cell development and function.
* **Development:** Neddylation is essential for normal embryonic development and tissue homeostasis.

Disruption of neddylation can lead to various diseases, including cancer, neurodegenerative disorders, and inflammatory diseases. Therefore, NEDD8 conjugation and its regulatory mechanisms are promising targets for therapeutic intervention in these conditions.'
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Proteins (4)

ProteinDefinitionTaxonomy
Endothelial PAS domain-containing protein 1An endothelial PAS domain-containing protein 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q99814]Homo sapiens (human)
DCN1-like protein 1A DCN1-like protein 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96GG9]Homo sapiens (human)
COP9 signalosome complex subunit 5A COP9 signalosome complex subunit 5 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q92905]Homo sapiens (human)
Hypoxia-inducible factor 1-alphaA hypoxia-inducible factor 1-alpha that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q16665]Homo sapiens (human)

Compounds (48)

CompoundDefinitionClassesRoles
ciclopiroxcyclic hydroxamic acid;
hydroxypyridone antifungal drug;
pyridone
antibacterial agent;
antiseborrheic
deferoxamineDeferoxamine: Natural product isolated from Streptomyces pilosus. It forms iron complexes and is used as a chelating agent, particularly in the mesylate form.

desferrioxamine B : An acyclic desferrioxamine that is butanedioic acid in which one of the carboxy groups undergoes formal condensation with the primary amino group of N-(5-aminopentyl)-N-hydroxyacetamide and the second carboxy group undergoes formal condensation with the hydroxyamino group of N(1)-(5-aminopentyl)-N(1)-hydroxy-N(4)-[5-(hydroxyamino)pentyl]butanediamide. It is a siderophore native to Streptomyces pilosus biosynthesised by the DesABCD enzyme cluster as a high affinity Fe(III) chelator.
acyclic desferrioxaminebacterial metabolite;
ferroptosis inhibitor;
iron chelator;
siderophore
carbonyl cyanide p-trifluoromethoxyphenylhydrazonecarbonyl cyanide p-trifluoromethoxyphenylhydrazone : A hydrazone that is hydrazonomalononitrile in which one of the hydrazine hydrogens is substituted by a p-trifluoromethoxyphenyl group.

Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone: A proton ionophore that is commonly used as an uncoupling agent in biochemical studies.
aromatic ether;
hydrazone;
nitrile;
organofluorine compound
ATP synthase inhibitor;
geroprotector;
ionophore
3-(5'-hydroxymethyl-2'-furyl)-1-benzylindazole3-(5'-hydroxymethyl-2'-furyl)-1-benzylindazole: antineoplastic; activates platelet guanylate cyclase; a radiosensitizing agent and guanylate cyclase activator; structure in first source

lificiguat : A member of the class of indazoles that is 1H-indazole which is substituted by a benzyl group at position 1 and a 5-(hydroxymethyl)-2-furyl group at position 3. It is an activator of soluble guanylate cyclase and inhibits platelet aggregation.
aromatic primary alcohol;
furans;
indazoles
antineoplastic agent;
apoptosis inducer;
platelet aggregation inhibitor;
soluble guanylate cyclase activator;
vasodilator agent
strophanthidinStrophanthidin: 3 beta,5,14-Trihydroxy-19-oxo-5 beta-card-20(22)-enolide. The aglycone cardioactive agent isolated from Strophanthus Kombe, S. gratus and other species; it is a very toxic material formerly used as digitalis. Synonyms: Apocymarin; Corchorin; Cynotoxin; Corchorgenin.14beta-hydroxy steroid;
19-oxo steroid;
3beta-hydroxy steroid;
5beta-hydroxy steroid;
cardenolides;
steroid aldehyde
cycloheximidecycloheximide : A dicarboximide that is 4-(2-hydroxyethyl)piperidine-2,6-dione in which one of the hydrogens attached to the carbon bearing the hydroxy group is replaced by a 3,5-dimethyl-2-oxocyclohexyl group. It is an antibiotic produced by the bacterium Streptomyces griseus.

Cycloheximide: Antibiotic substance isolated from streptomycin-producing strains of Streptomyces griseus. It acts by inhibiting elongation during protein synthesis.
antibiotic fungicide;
cyclic ketone;
dicarboximide;
piperidine antibiotic;
piperidones;
secondary alcohol
anticoronaviral agent;
bacterial metabolite;
ferroptosis inhibitor;
neuroprotective agent;
protein synthesis inhibitor
acriflavine chloride3,6-diamino-10-methylacridinium chloride : The 10-methochloride salt of 3,6-diaminoacridine. Note that a mixture of this compound with 3,6-diaminoacridine (proflavine) is known as acriflavine or neutral acriflavine.organic chloride saltantibacterial agent;
antiseptic drug;
carcinogenic agent;
histological dye;
intercalator
emetineemetine : A pyridoisoquinoline comprising emetam having methoxy substituents at the 6'-, 7'-, 10- and 11-positions. It is an antiprotozoal agent and emetic. It inhibits SARS-CoV2, Zika and Ebola virus replication and displays antimalarial, antineoplastic and antiamoebic properties.

Emetine: The principal alkaloid of ipecac, from the ground roots of Uragoga (or Cephaelis) ipecacuanha or U. acuminata, of the Rubiaceae. It is used as an amebicide in many different preparations and may cause serious cardiac, hepatic, or renal damage and violent diarrhea and vomiting. Emetine inhibits protein synthesis in EUKARYOTIC CELLS but not PROKARYOTIC CELLS.
isoquinoline alkaloid;
pyridoisoquinoline
antiamoebic agent;
anticoronaviral agent;
antiinfective agent;
antimalarial;
antineoplastic agent;
antiprotozoal drug;
antiviral agent;
autophagy inhibitor;
emetic;
expectorant;
plant metabolite;
protein synthesis inhibitor
phenethyl isothiocyanatephenethyl isothiocyanate : An isothiocyanate having a phenethyl group attached to the nitrogen. It is a naturally occurring compound found in some cruciferous vegetables (e.g. watercress) and is known to possess anticancer properties.

phenethyl isothiocyanate: a dietary liver aldehyde dehydrogenase inhibitor; promotes urinary bladder carcinoma
isothiocyanateantineoplastic agent;
EC 1.2.1.3 [aldehyde dehydrogenase (NAD(+))] inhibitor;
metabolite
topotecantopotecan : A pyranoindolizinoquinoline used as an antineoplastic agent. It is a derivative of camptothecin and works by binding to the topoisomerase I-DNA complex and preventing religation of these 328 single strand breaks.

Topotecan: An antineoplastic agent used to treat ovarian cancer. It works by inhibiting DNA TOPOISOMERASES, TYPE I.
pyranoindolizinoquinolineantineoplastic agent;
EC 5.99.1.2 (DNA topoisomerase) inhibitor
ursolic acidhydroxy monocarboxylic acid;
pentacyclic triterpenoid
geroprotector;
plant metabolite
puupehenone
panaxadiolpanaxadiol: a protopanaxadiol with the side chain cyclized into a pyran which is an artifact of acidic hydrolysis; RN refers to (3 beta,12 beta,20R)-isomertriterpenoid saponin
cryptopleurinecryptopleurine : An organic heteropentacyclic compound that is (14aR)-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline substituted at positions 2, 3 and 6 by methoxy groups.

cryptopleurine: plant bark alkaloid shown to inhibit protein synthesis; RN given refers to (R)-isomer; structure
alkaloid;
alkaloid antibiotic;
aromatic ether;
organic heteropentacyclic compound
antineoplastic agent;
antiviral agent;
protein synthesis inhibitor
8-mercaptoquinoline8-mercaptoquinoline: structure given in first source
tanshinonetanshinone: from root of Salvia miltiorrhiza Bunge; RN given refers to tanshinone I; cardioprotective agent and neuroprotective agentabietane diterpenoidanticoronaviral agent
celastrolmonocarboxylic acid;
pentacyclic triterpenoid
anti-inflammatory drug;
antineoplastic agent;
antioxidant;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
Hsp90 inhibitor;
metabolite
aaptamineaaptamine: natural product from sea sponge Aaptos aaptos; structure given in first source; RN from CA Index Guide 1984
xestoquinonexestoquinone: structure given in first source; RN given refers to the (S)-isomer; RN for cpd without isomeric designation not available 5/91; isolated from the sea sponge Xestospongia sapra
gl 331GL 331: structure in first source
tanshinone vitanshinone VI: isolated from the root of Salvia miltiorrhiza; structure in first source
cryptotanshinonecryptotanshinone: from Salvia miltiorrhizaabietane diterpenoidanticoronaviral agent
tanshinone ii atashinone IIA: a cardiovascular agent with antineoplastic activity; isolated from Salvia miltiorrhiza; structure in first sourceabietane diterpenoid
moracin mmoracin M: has been isolated from Morus alba L.; structure in first sourcebenzofurans
convallatoxinconvallatoxin : A cardenolide glycoside that consists of strophanthidin having a 6-deoxy-alpha-L-mannopyranosyl (L-rhamnosyl) group attached at position 3.

convallatoxin: PI: *CONVALLARIA (73-79)
14beta-hydroxy steroid;
19-oxo steroid;
5beta-hydroxy steroid;
alpha-L-rhamnoside;
steroid aldehyde;
steroid lactone
metabolite;
vasodilator agent
latrunculin alatrunculin A : A bicyclic macrolide natural product consisting of a 16-membered bicyclic lactone attached to the rare 2-thiazolidinone moiety. It is obtained from the Red Sea sponge Latrunculia magnifica and from the Fiji Islands sponge Cacospongia mycofijiensis. Latrunculin A inhibits actin polymerisation, microfilament organsation and microfilament-mediated processes.

latrunculin A: 16-membered macrolide attached to 2-thiazolidinone moiety; from Red Sea sponge Latrunculia magnifica; see also latrunculin B; structure given in first source
cyclic hemiketal;
macrolide;
oxabicycloalkane;
thiazolidinone
actin polymerisation inhibitor;
metabolite;
toxin
5-(4-chlorophenyl)-4h-1,2,4-triazole-3-thiol5-(4-chlorophenyl)-4H-1,2,4-triazole-3-thiol: a YUCCA enzyme inhibitor; structure in first sourcetriazoles
5-(4-methoxyphenyl)-1,2-dihydro-1,2,4-triazole-3-thionetriazoles
fm19g11FM19G11: structure in first sourcebenzamides
stattic1-benzothiophenes;
C-nitro compound;
sulfone
antineoplastic agent;
radiosensitizing agent;
STAT3 inhibitor
vomifoliol(6S,9R)-vomifoliol : A (6S)-vomifoliol with a R configuration for the hydroxy group at position 9.

blumenol A: a phytotoxin isolated from Oryza sativa Awaakamai; structure in first source

vomifoliol : A fenchane monoterpenoid that is 3,5,5-trimethylcyclohex-2-en-1-one substituted by a hydroxy and a (1E)-3-hydroxybut-1-en-1-yl group at position 4.
(6S)-vomifoliolmetabolite;
phytotoxin
mammeisinneoflavonoidmetabolite
17-(dimethylaminoethylamino)-17-demethoxygeldanamycin17-(dimethylaminoethylamino)-17-demethoxygeldanamycin: structure in first source

alvespimycin : A 19-membered macrocyle that is geldanamycin in which the methoxy group attached to the benzoquinone moiety has been replaced by a 2-(N,N-dimethylamino)ethylamino group.
1,4-benzoquinones;
ansamycin;
carbamate ester;
secondary amino compound;
tertiary amino compound
Hsp90 inhibitor
bakuchiolbakuchiol: chief component of Psoralea corylifolia Linn; structure
variolin bvariolin B: from Antartic sponge, Kirkpatrickia variolosa; structure in first source
haliclonadiaminehaliclonadiamine: from an Indonesian sponge Haliclona sp.; structure in first source
chetomin
manassantin bmanassantin B : A lignan isolated from Saururus cernuus and Saururus chinensis and has been shown to exhibit antineoplastic activity.

manassantin B: isolated from the roots of Saururus chinensis; structure in first source
benzodioxoles;
dimethoxybenzene;
lignan;
oxolanes;
secondary alcohol
antineoplastic agent;
metabolite
laurenditerpenollaurenditerpenol: from the tropical marine alga Laurenciaintricata; potently inhibits HIF-1 mediated hypoxic signaling in breast tumor cells; structure in first source
px 4782-amino-3-(4'-N,N-bis(2-chloroethyl)amino)phenylpropionic acid N-oxide: inhibits hypoxia-inducible factor-1alpha
103d5r103D5R: small-molecule inhibitor of the hypoxia-inducible factor 1 pathway; structure in first source
Dihydrotanshinone Idihydrotanshinone I: extracted from Radix Salviaeabietane diterpenoidanticoronaviral agent
Moracin Pbenzofurans
3,4-dimethoxy-n-((2,2-dimethyl-2h-chromen-6-yl)methyl)-n-phenylbenzenesulfonamide3,4-dimethoxy-N-((2,2-dimethyl-2H-chromen-6-yl)methyl)-N-phenylbenzenesulfonamide: has antineoplastic activity; structure in first source
k-strophanthosideK-strophanthoside: cardiac glycoside extracted from Strophanthus kombe; sugars (glucose-glucose-cymarose) are bonded with strophanthidin
ml228 probeML228 : A member of the class of 1,2,4-triazines in which the triazine ring is substituted at positions 3, 5, and 6 by pyridin-2-yl, ([biphenyl]-4-ylmethyl)amin, and methyl groups, respectively. It is an activator of the hypoxia inducible factor (HIF) pathway.

ML228 probe: structure in first source
1,2,4-triazines;
biphenyls;
pyridines;
secondary amino compound
hypoxia-inducible factor pathway activator
2-(3,4-dimethoxyphenyl)-1-(5-methoxy-2,2-dimethyl-2h-chromen-6-yl)ethanone2-(3,4-dimethoxyphenyl)-1-(5-methoxy-2,2-dimethyl-2H-chromen-6-yl)ethanone: an Hsp90 inhibitor; structure in first source
makaluvamine fmakaluvamine F: a potent & cytotoxic marine alkaloid; structure in first source