BP

GO:0006281

DNA repair

The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

NAS

BP

GO:0006302

double-strand break repair

The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.

IDA

BP

GO:0006734

NADH metabolic process

The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.

IMP

BP

GO:0006888

ER to Golgi vesicle-mediated transport

The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.

IEA

BP

GO:0006914

autophagy

The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.

IMP

BP

GO:0006919

activation of cysteine-type endopeptidase activity involved in apoptotic process

Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.

ISS

BP

GO:0006974

cellular response to DNA damage stimulus

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

IDA

BP

GO:0010918

positive regulation of mitochondrial membrane potential

Any process that activates or increases the frequency, rate or extent of establishment or extent of a mitochondrial membrane potential, the electric potential existing across any mitochondrial membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.

IMP

BP

GO:0016567

protein ubiquitination

The process in which one or more ubiquitin groups are added to a protein.

IDA|NAS

BP

GO:0018279

protein N-linked glycosylation via asparagine

The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.

IMP

BP

GO:0019079

viral genome replication

Any process involved directly in viral genome replication, including viral nucleotide metabolism.

IMP

BP

GO:0019985

translesion synthesis

The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.

IMP

BP

GO:0030433

ER-associated ubiquitin-dependent protein catabolic process

The chemical reactions and pathways resulting in the breakdown of proteins transported from the endoplasmic reticulum and targeted to cytoplasmic proteasomes for degradation. This process acts on misfolded proteins as well as in the regulated degradation of correctly folded proteins.

IDA|IMP|TAS

BP

GO:0030968

endoplasmic reticulum unfolded protein response

The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.

TAS

BP

GO:0030970

retrograde protein transport, ER to cytosol

The directed movement of unfolded or misfolded proteins from the endoplasmic reticulum to the cytosol through the translocon.

IDA|IMP

BP

GO:0031334

positive regulation of protein complex assembly

Any process that activates or increases the frequency, rate or extent of protein complex assembly.

IDA

BP

GO:0032436

positive regulation of proteasomal ubiquitin-dependent protein catabolic process

Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.

IDA

BP

GO:0034214

protein hexamerization

The formation of a protein hexamer, a macromolecular structure consisting of six noncovalently associated identical or nonidentical subunits.

IEA

BP

GO:0036503

ERAD pathway

The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein modifications necessary for correct substrate transfer (e.g. ubiquitination), transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.

IDA|IMP

BP

GO:0042981

regulation of apoptotic process

Any process that modulates the occurrence or rate of cell death by apoptotic process.

TAS

BP

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.

IMP|NAS

BP

GO:0045184

establishment of protein localization

The directed movement of a protein to a specific location.

TAS

BP

GO:0045732

positive regulation of protein catabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.

IDA

BP

GO:0046034

ATP metabolic process

The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.

IEA

BP

GO:0051260

protein homooligomerization

The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.

IEA

BP

GO:0070842

aggresome assembly

The aggregation, arrangement and bonding together of a set of components to form an aggresome; requires the microtubule cytoskeleton and dynein.

IEA

BP

GO:0070987

error-free translesion synthesis

The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.

TAS

BP

GO:0071712

ER-associated misfolded protein catabolic process

The chemical reactions and pathways resulting in the breakdown of misfolded proteins transported from the endoplasmic reticulum and targeted to cytoplasmic proteasomes for degradation.

IMP

BP

GO:0072389

flavin adenine dinucleotide catabolic process

The chemical reactions and pathways resulting in the breakdown of flavin adenine dinucleotide, which acts as a coenzyme or prosthetic group of various flavoprotein oxidoreductase enzymes.

IMP

BP

GO:0097352

autophagosome maturation

The process in which autophagosomes, double-membraned vacuoles containing cytoplasmic material fuse with a vacuole (yeast) or lysosome (e.g. mammals and insects). In the case of yeast, inner membrane-bounded structures (autophagic bodies) appear in the vacuole. Fusion provides an acidic environment and digestive function to the interior of the autophagosome.

IMP

BP

GO:1903006

positive regulation of protein K63-linked deubiquitination

Any process that activates or increases the frequency, rate or extent of protein K63-linked deubiquitination.

IDA

BP

GO:1903007

positive regulation of Lys63-specific deubiquitinase activity

Any process that activates or increases the frequency, rate or extent of Lys63-specific deubiquitinase activity.

IDA

BP

GO:1903715

regulation of aerobic respiration

Any process that modulates the frequency, rate or extent of aerobic respiration.

IMP

BP

GO:1903862

positive regulation of oxidative phosphorylation

Any process that activates or increases the frequency, rate or extent of oxidative phosphorylation.

IMP

BP

GO:2000158

positive regulation of ubiquitin-specific protease activity

Any process that activates or increases the frequency, rate or extent of ubiquitin-specific protease (deubiquitinase) activity.

IEA

BP

GO:2001171

positive regulation of ATP biosynthetic process

Any process that activates or increases the frequency, rate or extent of ATP biosynthetic process.

IMP

CC

GO:0000502

proteasome complex

A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.

IDA

CC

GO:0005634

nucleus

A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

IDA|TAS

CC

GO:0005654

nucleoplasm

That part of the nuclear content other than the chromosomes or the nucleolus.

IDA|TAS

CC

GO:0005737

cytoplasm

All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

IDA

CC

GO:0005783

endoplasmic reticulum

The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

IDA

CC

GO:0005789

endoplasmic reticulum membrane

The lipid bilayer surrounding the endoplasmic reticulum.

IDA

CC

GO:0005811

lipid particle

An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.

IDA

CC

GO:0005829

cytosol

The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

IDA|TAS

CC

GO:0034098

VCP-NPL4-UFD1 AAA ATPase complex

A multiprotein ATPase complex required for the efficient dislocation of ER-lumenal degradation substrates, and their subsequent proteolysis by the proteasome. In budding yeast, this complex includes Cdc48p, Npl4p and Ufd1p proteins. In mammals, this complex includes a hexamer of VCP/p97 (a cytosolic ATPase) and trimers of each of its cofactors UFD1L and NPL4 (NPLOC4) (e.g. a 6:3:3 stoichiometry).

ISS|TAS

CC

GO:0035861

site of double-strand break

A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.

IDA

CC

GO:0036513

Derlin-1 retrotranslocation complex

A protein complex that functions in the retrotranslocation step of ERAD (ER-associated protein degradation), and includes at its core Derlin-1 oligomers forming a retrotranslocation channel.

IDA

CC

GO:0043209

myelin sheath

An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

IEA

CC

GO:0043231

intracellular membrane-bounded organelle

Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

ISS

CC

GO:0048471

perinuclear region of cytoplasm

Cytoplasm situated near, or occurring around, the nucleus.

IDA

CC

GO:0070062

extracellular exosome

A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

IDA

CC

GO:1990730

VCP-NSFL1C complex

A protein complex between the ATPase VCP (p97) and its cofactor p47 (NSFL1C). In human, the protein complex consists of one homotrimer of NSFL1C/p47 per homohexamer of VCP/p97.

ISS

MF

GO:0005515

protein binding

Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

IPI

MF

GO:0005524

ATP binding

Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

IEA

MF

GO:0008289

lipid binding

Interacting selectively and non-covalently with a lipid.

IEA

MF

GO:0016887

ATPase activity

Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.

IMP|TAS

MF

GO:0019903

protein phosphatase binding

Interacting selectively and non-covalently with any protein phosphatase.

IPI

MF

GO:0019904

protein domain specific binding

Interacting selectively and non-covalently with a specific domain of a protein.

IPI

MF

GO:0031593

polyubiquitin binding

Interacting selectively and non-covalently with a polymer of ubiqutin.

IDA

MF

GO:0031625

ubiquitin protein ligase binding

Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.

IPI

MF

GO:0035800

deubiquitinase activator activity

Increases the activity of deubiquitinase, an enzyme that catalyzes the hydrolysis of various forms of polymeric ubiquitin sequences.

IDA

MF

GO:0036435

K48-linked polyubiquitin binding

Interacting selectively and non-covalently and non-covalently with a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers.

IEA

MF

GO:0042288

MHC class I protein binding

Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.

IEA

MF

GO:0042802

identical protein binding

Interacting selectively and non-covalently with an identical protein or proteins.

IPI

MF

GO:0043531

ADP binding

Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.

IEA

MF

GO:0044389

ubiquitin-like protein ligase binding

Interacting selectively and non-covalently with a ubiquitin-like protein ligase, such as ubiquitin-ligase.

IPI

MF

GO:0044822

poly(A) RNA binding

Interacting non-covalently with a poly(A) RNA, a RNA molecule which has a tail of adenine bases.

IDA

MF

GO:1904288

BAT3 complex binding

Interacting selectively and non-covalently with a BAT3 complex.

IPI

MF

GO:1990381

ubiquitin-specific protease binding

Interacting selectively and non-covalently with a ubiquitin-specific protease.

IPI