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PDBsum entry 5bnb
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Contents |
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150 a.a.
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76 a.a.
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72 a.a.
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68 a.a.
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116 a.a.
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a ube2s-Ubiquitin conjugate.
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Authors
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S.Lorenz,
M.Bhattacharyya,
C.Feiler,
M.Rape,
J.Kuriyan.
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Ref.
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Plos One, 2016,
11,
e0147550.
[DOI no: ]
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PubMed id
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Abstract
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Protein ubiquitination occurs through the sequential formation and
reorganization of specific protein-protein interfaces. Ubiquitin-conjugating
(E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage
between the C-terminus of a "donor" ubiquitin and a primary amino
group of an "acceptor" ubiquitin molecule. This reaction involves an
intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound
to the active site cysteine of the E2 and a functionally important interface is
formed between the two proteins. A docked model of a Ube2S-donor ubiquitin
complex was generated previously, based on chemical shift mapping by NMR, and
predicted contacts were validated in functional studies. We now present the
crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains
an interface between Ube2S and ubiquitin in trans that resembles the earlier
model in general terms, but differs in detail. The crystallographic interface is
more hydrophobic than the earlier model and is stable in molecular dynamics (MD)
simulations. Remarkably, the docked Ube2S-donor complex converges readily to the
configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since
the crystallographic interface is fully consistent with mutational effects, this
indicates that the structure provides an energetically favorable representation
of the functionally critical Ube2S-donor interface.
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