SCUD (Saccharomyces Cerevisiae Ubiquitination Database)

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Database Menu Entries
A user's query is searched through the search space and the field that the user specifies. "Interactive mode" check will show the search result as soon as any character is typed in. The interactive mode might be a little bit slow on Mozilla Firefox web browser.
It is linked to the page which shows a list of ubiquitination enzymes. It includes an E1 ubiquitin activating enzyme, E2 ubiquitin-conjugating enzymes, E3 ubiquitin-protein ligases, and deubiquitination enzymes (DUB). Especially E3 ubiquitin-protein ligases are categorized into sevaral E3 types in accordance with their unique domain or complex-type. Each E3 type contains substrate receptors which are responsible for the substrate recognition. Hypertext links will provide more descriptive explanations for each enzyme or substrate receptor.
It is linked to the page which shows a list of wild-type and mutant ubiquitinated substrates. Detail descriptions on ubiquitination features as well as general protein information of each substrate are provided by a hypertext link.
Ubiquitination types
Its link shows all the ubiquitination types found in the substrates of this database. Ubiquitination process can be divided into several types according to its topolgy. A hyper link for each type will provide a list of substrates ubiquitinated by this ubiquitination type.
Users can run the BLAST program against all the sequences in this database including enzymes and substrates. Search space can be limited to the specific enzyme classes or substrates. It will be helpful to cross-species research on the ubiquitination system.
In addition to the regular database update, researchers in ubiquitination field also can contribute to the database by submitting new proteins including enzymes and substrates, and by finding errors to be corrected. Moreover, database users are expected to submit general opinions and suggestions about the database itself.
Ubiquitination Terminologies
Mutant name
Mutant protein name which is found in the literature dealing with ubiquitinated mutant substrates. Note that a wild-type substrate can have multiple mutant names. Example mutant names are PDR5*, PMA1-7, and PMA1-D378N.
Ubiquitination site
Experimently verified ubiquitinated lysines are denoted. Some of lysines produce more effective ubiquitination result when multiple lysines on a substrate can be ubiquitinated simultaneously.
Ubiquitination type
Ubiquitination types are categorized based on the number of ubiquitin moieties involved, the number of lysines simultaneously ubiquitinated on a substrate, the chain topology when a ubiquitin-chain is generated, and the relation between substrate and substrate receptor.
E2 ubiquitin-conjugating enzyme
E2 type enzymes receive a ubiquitin activated by E1 enzyme, and actually catalyze the attachment of a ubiquitin to the substrate.
E3 class
E3 ubiquitin-protein ligase enzymes function as the substrate recognition modules of the ubiquitination system and are capable of interaction with both E2 and substrate. E3 enzymes possess one of two domains:
  • The HECT (Homologous to the E6-AP Carboxyl Terminus) domain.
  • The RING (Really Interesting New Gene) domain.
We defined two E3 classes (HECT and RING) and classified the E3 enzymes into the classes, to which they belong.
E3 subclass
RING class E3 enzymes can be further divided into E3 subclasses.
  • SPRF (Single Protein RING Finger): This type of E3 enzymes function as a unit protein. They possess both the substrate recognition part and the E2 interaction part on them.
  • SCF (SKP1, CDC53, and F-box): Cullin (CDC53)-dependent multi-subunit E3 enzyme complex. F-box proteins are involved in the recognition of substrates.
  • ECS (ELC1, CUL3, and SOCS/BC-box): Cullin (CUL3)-dependent multi-subunit E3 enzyme complex. SOCS/BC-box proteins are involved in the recognition of substrates.
  • U-BOX: This type of E3 enzymes have U-box domain. They have been known to act as E4, but their pure E3 activity is being reported recently.
  • APC (Anaphase Promoting Complex): Multi-subunit E3 enzyme complex. Its subunit "APC2" is similar with Cullins in SCF and ECS complex.
Substrate receptor
Each E3 type comprises various substrate receptors which play a role in specific interaction with the substrates. For example, SCF type consists of various F-box protein(substrate receptor) such as CDC4 and GRR1.
Ubiquitin receptor
Ubiquitinated proteins are recognized by families of ubiquitin receptors, and targeted to various cellular complexes such as proteasome and vacuole. Ubiquitin receptors usually contain the domains such as UBA, UIM, and U-box which interact with ubiquitins attached to the substrates. In yeast, there are at least five potential receptors (DDI1, DSK2, RAD23, RPN10, and RPT5) plus a set of CDC48-based complexes, including CDC48-NPL4-UFD1.
Deubiquitination enzyme (DUB)
DUB enzymes function to remove ubiquitin from substrate proteins, thus rescuing them from degradation.
Ubiquitination effect
Ubiquitination is involved in a variety of biological processes including protein degradation. "Ubiquitination effect" explains the result of corresponding substrate ubiquitination.
Experimental Evidences
Protein stability assay
Ubiquitin-modified proteins are likely to be degraded by proteasome or vacuole. This experimental result shows the stability change of the protein of interest. However, it cannot directly give the evidence whether this protein is ubiquitinated.
Interaction assay
Potential ubiquitinated proteins first should interact with E2 and E3 enzymes to be ubiquitinated. Therefore, if a protein interacts with E3 enzymes, this fact can be a weak evidence that the protein is ubiquitinated.
Localization assay
Since the ubiquitination plays a role in sorting proteins to specific locations such as vacuole, it can be assumed that a protein is ubiquitinated if the protein is transferred to a certain location after experimental settings.
High MW product confirmation
If a protein is modified by ubiquitins, its molecular weight will increase. High molecular weight products can be confirmed by experimental techniques such as Western Blot and autoradiography.
Ub-conjugate confirmation
High molecular weight products which appear in gel electrophoresis experiments can be further confirmed as ubiquitin conjugates using epitope-tagged ubiquitins and anti-ubiquitin antibodies. This result provides more reliable evidence that proteins of interest are ubiquitinated.
Purification & protein ID
Ubiquitin-conjugates are purified by various methods, and usually the LC/MS technique is applied to identify the purified proteins.