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PDBsum entry 2gmi
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Ligase, human protein
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PDB id
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2gmi
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Contents |
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152 a.a.
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135 a.a.
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76 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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Mms2-Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-Specific polyubiquitin chain formation.
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Authors
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M.J.Eddins,
C.M.Carlile,
K.M.Gomez,
C.M.Pickart,
C.Wolberger.
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Ref.
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Nat Struct Mol Biol, 2006,
13,
915-920.
[DOI no: ]
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PubMed id
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Abstract
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Lys63-linked polyubiquitin chains participate in nonproteolytic signaling
pathways, including regulation of DNA damage tolerance and NF-kappaB activation.
E2 enzymes bound to ubiquitin E2 variants (UEV) are vital in these pathways,
synthesizing Lys63-linked polyubiquitin chains, but how these complexes achieve
specificity for a particular lysine linkage has been unclear. We have determined
the crystal structure of an Mms2-Ubc13-ubiquitin (UEV-E2-Ub) covalent
intermediate with donor ubiquitin linked to the active site residue of Ubc13. In
the structure, the unexpected binding of a donor ubiquitin of one Mms2-Ubc13-Ub
complex to the acceptor-binding site of Mms2-Ubc13 in an adjacent complex allows
us to visualize at atomic resolution the molecular determinants of
acceptor-ubiquitin binding. The structure reveals the key role of Mms2 in
allowing selective insertion of Lys63 into the Ubc13 active site and suggests a
molecular model for polyubiquitin chain elongation.
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Figure 1.
Figure 1. The structure of the Mms2–Ubc13-Ub complex. (a)
Blue, Mms2; magenta, Ubc13; orange, the covalently attached
donor ubiquitin. TheC terminus of the donor ubiquitin, Gly76, is
covalently attached to active site residue Ser87 of Ubc13(C87S).
(b) Packing interactions between complexes in the crystal. One
Mms2–Ubc13(C87S)-Ub complex is drawn as a surface
representation (same coloring as in a) and an adjacent complex
as ribbons (turquoise, Mms2; red, Ubc13; green, ubiquitin), to
show packing in the crystal. The latter ubiquitin (green) binds
in the acceptor site of the Mms2 from an adjacent complex
(blue). Lys63 of this acceptor ubiquitin lies in the active site
near the ester linkage.
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Figure 2.
Figure 2. Molecular details of linkage selectivity. (a)
Active site of the E2 is shown with the covalent ester linkage
between Ser87 of Ubc13(C87S) (magenta) and the C-terminal Gly76
of the donor ubiquitin (orange). Lys63 of the acceptor ubiquitin
is in green. Electron density shown is from a simulated
annealing omit map with F[o] - F[c] density contoured at 3  .
Omitted residues included Gly74–Gly76 of ubiquitin, the side
chain of Ser87 of Ubc13 and side chain atoms within 5 Å of
the omitted residues. (b) Hydrogen bonds (dashed lines) help
position the acceptor Lys63 in the active site of Ubc13 with the
C terminus of the donor ubiquitin. (c) The interface between
Mms2 (blue) and the acceptor ubiquitin is shown, with residues
that affect acceptor-ubiquitin binding shown in turquoise for
Mms2 (Ser27, Thr44, Ile57) and bright green for ubiquitin
(Ile44).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2006,
13,
915-920)
copyright 2006.
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