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PDBsum entry 2j4x
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Signaling protein
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PDB id
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2j4x
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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 streptococcus dysgalactiae-Derived mitogen reveals a zinc-Binding site and alterations in tcr binding.
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Authors
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S.Saarinen,
H.Kato,
T.Uchiyama,
T.Miyoshi-Akiyama,
A.C.Papageorgiou.
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Ref.
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J Mol Biol, 2007,
373,
1089-1097.
[DOI no: ]
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PubMed id
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Abstract
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Bacterial superantigens are protein toxins with an ability to cause serious
diseases in humans by activating a large number of T cells. Streptococcus
dysgalactiae-derived mitogen (SDM) is a novel superantigen that is distinct from
other known superantigens based on phylogenetic analysis. The X-ray structure of
SDM has been determined at 1.95 A resolution. SDM shares the same characteristic
fold with other superantigens, but it shows a major structural difference due to
the lack of the alpha5 helix between the beta10 and beta11 strands. A bound zinc
ion was identified in the structure at the C-terminal domain of the molecule.
SDM appears to bind to the major histocompatibility complex class II beta-chain
through the zinc-binding site, as described by mutagenesis data and structural
comparisons. T-cell binding instead shows a significant difference compared to
other superantigens. The mutation of Asn11 (a conserved residue that is known to
be significant for T-cell-receptor binding in other superantigens) and Lys15 to
Ala did not cause any decrease in the mitogenic activity of SDM. This
observation and the lack of the alpha5 helix suggest alterations in
T-cell-receptor binding.
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Figure 3.
Fig. 3. Cα atom stereodiagram of SDM superimposed onto SPE-C
and SMEZ-2. SDM, black; SPE-C, red; SMEZ-2, yellow.
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Figure 4.
Fig. 4. The zinc-binding site of SDM. (a) Difference electron
density map based on anomalous scattering. (b) The zinc-binding
site of SDM on the final 2|F[o]|−|F[c]| electron density map.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
373,
1089-1097)
copyright 2007.
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