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PDBsum entry 2mro
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Transport protein/signaling protein
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PDB id
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2mro
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References listed in PDB file
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Key reference
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Title
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Dna-Damage-Inducible 1 protein (ddi1) contains an uncharacteristic ubiquitin-Like domain that binds ubiquitin.
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Authors
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U.Nowicka,
D.Zhang,
O.Walker,
D.Krutauz,
C.A.Castañeda,
A.Chaturvedi,
T.Y.Chen,
N.Reis,
M.H.Glickman,
D.Fushman.
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Ref.
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Structure, 2015,
23,
542-557.
[DOI no: ]
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PubMed id
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Abstract
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Ddi1 belongs to a family of shuttle proteins targeting polyubiquitinated
substrates for proteasomal degradation. Unlike the other proteasomal shuttles,
Rad23 and Dsk2, Ddi1 remains an enigma: its function is not fully understood and
structural properties are poorly characterized. We determined the structure and
binding properties of the ubiquitin-like (UBL) and ubiquitin-associated (UBA)
domains of Ddi1 from Saccharomyces cerevisiae. We found that while Ddi1UBA forms
a characteristic UBA:ubiquitin complex, Ddi1UBL has entirely uncharacteristic
binding preferences. Despite having a ubiquitin-like fold, Ddi1UBL does not
interact with typical UBL receptors but unexpectedly binds ubiquitin, forming a
unique interface mediated by hydrophobic contacts and by salt bridges between
oppositely charged residues of Ddi1UBL and ubiquitin. In stark contrast to
ubiquitin and other UBLs, the β-sheet surface of Ddi1UBL is negatively charged
and therefore is recognized in a completely different way. The dual
functionality of Ddi1UBL, capable of binding both ubiquitin and proteasome,
suggests an intriguing mechanism for Ddi1 as a proteasomal shuttle.
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