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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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PDB id:
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Cell cycle
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Title:
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Crystal structure of a ube2s-ubiquitin conjugate
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Structure:
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Ubiquitin-conjugating enzyme e2 s. Chain: a, b, c, d. Synonym: e2-epf,ubiquitin carrier protein s,ubiquitin-conjugating enzyme e2-24 kda,ubiquitin-conjugating enzyme e2-epf5,ubiquitin- protein ligase s. Engineered: yes. Mutation: yes. Polyubiquitin-b. Chain: e, f, g, i.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2s, e2epf, ok/sw-cl.73. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ubb.
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Resolution:
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2.49Å
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R-factor:
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0.246
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R-free:
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0.304
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Authors:
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S.G.Lorenz,C.G.Feiler,J.Kuriyan
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Key ref:
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S.Lorenz
et al.
(2016).
Crystal Structure of a Ube2S-Ubiquitin Conjugate.
Plos One,
11,
e0147550.
PubMed id:
DOI:
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Date:
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25-May-15
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Release date:
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17-Feb-16
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PROCHECK
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Headers
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References
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Q16763
(UBE2S_HUMAN) -
Ubiquitin-conjugating enzyme E2 S from Homo sapiens
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Seq:
Struc:
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222 a.a.
150 a.a.*
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P0CG47
(UBB_HUMAN) -
Polyubiquitin-B from Homo sapiens
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Seq:
Struc:
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229 a.a.
76 a.a.
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P0CG47
(UBB_HUMAN) -
Polyubiquitin-B from Homo sapiens
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Seq:
Struc:
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229 a.a.
72 a.a.
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Enzyme class:
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Chains A, B, C, D:
E.C.2.3.2.23
- E2 ubiquitin-conjugating enzyme.
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Reaction:
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S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L- cysteine
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DOI no:
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Plos One
11:e0147550
(2016)
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PubMed id:
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Crystal Structure of a Ube2S-Ubiquitin Conjugate.
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S.Lorenz,
M.Bhattacharyya,
C.Feiler,
M.Rape,
J.Kuriyan.
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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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