Ubiquitin

What InterPro Tells Us

The sequence of ubiquitin is highly conserved form protozoan to vertebrates. In most species there are many genes coding for UB, which can be divided into two classes: class 1 produce poly-UB molecules consisting of a variable number of head-to-tail repeats of UB, while class 2 produces proteins consisting of a single copy of UB fused to a C-terminal extension protein (CEP), which is usually a ribosomal protein. In addition, several UB-like molecules (Ubls) have been identified. These Ubls can be can be divided into two subclasses: type 1 Ubls such as SUMO1 and NEDD8 are small in size and can be ligated to target proteins in much the same many as UB, while type 2 Ubls contain UB-like structure in a variety of different classes of large proteins, such s Rad23, Elongin B and Parkin.

P42739 Green Algae Ubiquitin

InterPro Domain Architecture

InterPro Entry	Method Accession	Graphical Match	Method Name
IPR000626	PF00240		ubiquitin
IPR000626	PR00348		UBIQUITIN
IPR000626	PS00299		UBIQUITIN_1
IPR000626	PS50053		UBIQUITIN_2
IPR000626	SM00213		UBQ
	SWISS‑MODEL Entry	SWISS‑MODEL Prediction
	P42739

From the graphical match above, you can see that the signatures (method accession) are all from one InterPro entry, IPR000626 for Ubiquitin. This entry represents not only UB, but also any protein that contains a homologous UB-like domain, such as Parkin, IkBb kinase, neddylin (NEDD8), Rad23, Bat3, and Dsk2, amongst others. As such, this entry represents the ubiquitin “domain”, where the ubiquitin monomer consists of this domain on its own. There are five signatures representing this domain: PF00240 from the PFAM database, PR00348 from the PRINTS database, PS00299 and PS50053 from the PROSITE database, and SM00213 from the SMART database. Most of these signatures represent the full length of the ubiquitin domain, except for PS00299, which is based on conserved positions in the central section of the sequence.

There are no structures for this ubiquitin molecule in the Protein Data Bank (PDB), although there are several structures for proteins containing UB-like domains. However, InterPro provides a prediction of the structure of ubiquitin in the form of a SWISS-MODEL homology model. It should be noted that the SWISS-MODEL data must be considered with care, because the results of any modelling procedure is predictive.

What the Structure Tells Us

There are structures available in PDB for proteins containing ubiquitin-like domains. A detailed description and visualisation of the structural features of ubiquitin based on this data can be found at PDB ‘Molecule of the Month’.

Next: Table of Ubiquitin Proteins and Their Processing Enzymes

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