Uba1

Function

Uba1 is an E1 protein involved in the ubiquitination pathway found in Saccharomyces cerevisia, baker’s yeast^{[1] [2] [3] [4]} Ubiquitination, a post-translational modification that conjugates ubiquitin to a target protein, has been shown to have important cellular effects, such as the marking of a protein for degradation ^[1]. Ubiquitination is carried out in a three step enzymatic cascade ^[2] that utilizes E1, E2, and E3 enzymes. The ubiquitin cascade starts when E1 is adenylated at its carboxyl terminal glycine3, then the ubiquitin is linked to a cysteine in the E1 resulting in an E1~Ub thioester bond ^{[2] [4] [3]}. This ATP consuming step is followed by a ubiquitin transfer to an E2. An E3 enzyme, along with E2, then catalyzes (induces) the ubiquitination of the target protein. ^{[4] [1]}

Ubiquitin Interactions

The of Uba1 consists of six structural domains (IAD, AAD, FCCH, SCCH, 4HB, and UFD), four of which pack together to create a central cavity. The cavity is divided into two distinct clefts (left and right) by the SCCH/AAD linker fragment. Uba1 exists as a in solution, with two monomers interacting in a noncovalent manner. Ubiquitin binds to the cysteine located on the right cleft of Uba1 which allows for Ubiquitin to orient itself relative to the active site located on the left cleft. The structure of results in a change in conformation that buries a significant portion of Uba1 exposed surface area. The located on the SCCH domain of Uba1 forms a thioester with the C-terminus of Ubiquitin. It is suggested that a significant conformation change occurs when Ubiquitin binds to Uba1 due to the large distance (~35 Å) between the catalytic cysteine residue and the adenylation active site.

Aside from the catalytic site interactions there are two main interactions between ubiquitin and UBA11, a hydrophobic interface, and the polar interface between ubiquitin and first-catalytic cysteine half domain, FCCH, which contains the E1 active site cysteine. The are maximized by interactions between the Phe898, Leu903, and Phe905 on UBA1 and the Leu8, Ile44 and Val70 residues on ubiquitin1. This interaction is further stabilized by a between the Asn900 residue on UBA1 and the carbonyl oxygen of ubiquitin’s Leu81. The interaction between ubiquitin’s c-terminus and the FCCH domain of UBA1 relies on a deep groove formed from residues 175-265 in UBA11. Four polar residues on ubiquitin, Lys11, Thr12, Gln31, and Asp32, form hydrogen bonds with three polar residues, Arg202, Gly204, and Glu206, of UBA1.1 ^[1]

E2 interactions

When Ubiquitin binds, Uba1 then coordinates the transfer of Ubiquitin onto an E2 enzyme. The E2 enzyme (seen in pink) with Uba1 in the cavity where a transthioesterfication of Ubiquitin from the catalytic cysteine of Uba1 to the catalytic cysteine of the E2 occurs. The E2, in conjunction with the E3 enzyme, transfers the Ubiquitin onto its final substrate.^{[1] [5]}

References

1. ↑ ^{1.0 1.1 1.2 1.3 1.4} Lee I, Schindelin H. Structural Insights into E1-Catalyzed Ubiquitin Activation and Transfer to Conjugating Enzymes. Cell 134, 268–278 (2008).
2. ↑ ^{2.0 2.1 2.2} Groettrup, M.; Pelzer, C.; Schmidtke, G.; Hofmann, K. Activating the ubiquitin family: UBA6 challenges the field. Trends Biochem. Sci. 2008, 33, 230-237. DOI:http://dx.doi.org/10.1016/j.tibs.2008.01.005
3. ↑ ^{3.0 3.1} Chen, Z. J.; Sun, L. J. Nonproteolytic Functions of Ubiquitin in Cell Signaling. Mol. Cell 2009, 33, 275-286. DOI:http://dx.doi.org/10.1016/j.molcel.2009.01.014.
4. ↑ ^{4.0 4.1 4.2} McGrath, J. P.; Jentsch, S.; Varshavsky, A. UBA 1: an essential yeast gene encoding ubiquitin-activating enzyme. EMBO J. 1991, 10, 227-236.
5. ↑ Walden H, Podgorski MS, Huang DT, Miller DW, Howard RJ, Minor DL Jr, Holton JM, Schulman BA. The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Molecular Cell 12, 1427–1437 (2003).