2i1a
From Proteopedia
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A Retroviral Protease-Like Domain in the Eukaryotic Protein Ddi1
Overview
Retroviral aspartyl proteases are homodimeric, whereas eukaryotic aspartyl, proteases tend to be large, monomeric enzymes with 2-fold internal, symmetry. It has been proposed that contemporary monomeric aspartyl, proteases evolved by gene duplication and fusion from a primordial, homodimeric enzyme. Recent sequence analyses have suggested that such, "fossil" dimeric aspartyl proteases are still encoded in the eukaryotic, genome. We present evidence for retention of a dimeric aspartyl protease, in eukaryotes. The X-ray crystal structure of a domain of the, Saccharomyces cerevisiae protein Ddi1 shows that it is a dimer with a fold, similar to that of the retroviral proteases. Furthermore, the double, Asp-Thr-Gly-Ala amino acid sequence motif at the active site of HIV, protease is found with identical geometry in the Ddi1 structure. However, the putative substrate binding groove is wider in Ddi1 than in the, retroviral proteases, suggesting that Ddi1 accommodates bulkier, substrates. Ddi1 belongs to a family of proteins known as the ubiquitin, receptors, which have in common the ability to bind ubiquitinated, substrates and the proteasome. Ubiquitin receptors contain an, amino-terminal ubiquitin-like (UBL) domain and a carboxy-terminal, ubiquitin-associated (UBA) domain, but Ddi1 is the only representative in, which the UBL and UBA domains flank an aspartyl protease-like domain. The, remarkable structural similarity between the central domain of Ddi1 and, the retroviral proteases, in the global fold and in active-site detail, suggests that Ddi1 functions proteolytically during regulated protein, turnover in the cell.
About this Structure
2I1A is a Single protein structure of sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.
Reference
Ddi1, a eukaryotic protein with the retroviral protease fold., Sirkis R, Gerst JE, Fass D, J Mol Biol. 2006 Dec 1;364(3):376-87. Epub 2006 Sep 3. PMID:17010377
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