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PDBsum entry 1ddt
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References listed in PDB file
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Key reference
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Title
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Refined structure of dimeric diphtheria toxin at 2.0 a resolution.
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Authors
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M.J.Bennett,
S.Choe,
D.Eisenberg.
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Ref.
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Protein Sci, 1994,
3,
1444-1463.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
87%.
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Abstract
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The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution,
based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor
of 19.5% with a model obeying standard geometry. The refined model consists of
523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl
3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The
2.0-A refined model reveals that the binding motif for ApUp includes residues in
the catalytic and receptor-binding domains and is different from the Rossmann
dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52)
that crosses the active site. Several residues in the active site were
previously identified as NAD-binding residues. Glu 148, previously identified as
playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is
about 5 A from uracil in ApUp. The trigger for insertion of the transmembrane
domain of DT into the endosomal membrane at low pH may involve 3 intradomain and
4 interdomain salt bridges that will be weakened at low pH by protonation of
their acidic residues. The refined model also reveals that each molecule in
dimeric DT has an "open" structure unlike most globular proteins, which we call
an open monomer. Two open monomers interact by "domain swapping" to form a
compact, globular dimeric DT structure. The possibility that the open monomer
resembles a membrane insertion intermediate is discussed.
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Secondary reference #1
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Title
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Domain swapping: entangling alliances between proteins.
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Authors
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M.J.Bennett,
S.Choe,
D.Eisenberg.
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Ref.
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Proc Natl Acad Sci U S A, 1994,
91,
3127-3131.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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The crystal structure of diphtheria toxin.
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Authors
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S.Choe,
M.J.Bennett,
G.Fujii,
P.M.Curmi,
K.A.Kantardjieff,
R.J.Collier,
D.Eisenberg.
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Ref.
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Nature, 1992,
357,
216-222.
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PubMed id
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