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PDBsum entry 2vbk
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Viral protein
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PDB id
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2vbk
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References listed in PDB file
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Key reference
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Title
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An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of shigella flexneri phage sf6.
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Authors
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J.J.Müller,
S.Barbirz,
K.Heinle,
A.Freiberg,
R.Seckler,
U.Heinemann.
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Ref.
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Structure, 2008,
16,
766-775.
[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
92%.
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Abstract
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Sf6 belongs to the Podoviridae family of temperate bacteriophages that infect
gram-negative bacteria by insertion of their double-stranded DNA. They attach to
their hosts specifically via their tailspike proteins. The 1.25 A crystal
structure of Shigella phage Sf6 tailspike protein (Sf6 TSP) reveals a conserved
architecture with a central, right-handed beta helix. In the trimer of Sf6 TSP,
the parallel beta helices form a left-handed, coiled-beta coil with a pitch of
340 A. The C-terminal domain consists of a beta sandwich reminiscent of viral
capsid proteins. Further crystallographic and biochemical analyses show a
Shigella cell wall O-antigen fragment to bind to an endorhamnosidase active site
located between two beta-helix subunits each anchoring one catalytic
carboxylate. The functionally and structurally related bacteriophage, P22 TSP,
lacks sequence identity with Sf6 TSP and has its active sites on single
subunits. Sf6 TSP may serve as an example for the evolution of different host
specificities on a similar general architecture.
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Figure 2.
Figure 2. Structural Comparison of Sf6 TSP and P22 TSP
Crystal structures of the monomers and biologically active
trimers of Sf6 TSPΔN (A and C), and of P22 TSPΔN (B and D)
(PDB code: 1TSP [Steinbacher et al., 1994]). The view is
perpendicular to the trimer axis onto the intersubunit cleft
(rotated by  vert,
similar 45° relative to Figure 1).
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Figure 6.
Figure 6. Localization of the Endorhamnosidase Active Site of
Sf6 TSPΔN
(A) Difference electron density (contoured at
3σ) observed in a complex of the protein with one repeating
unit (RU) of an O-antigen hydrolysis product
(α-l-Rhap-(1-3)-β-l-GlcpNAc-(1-2)-α-l-Rhap-(1-2)-α-l-Rhap).
The sugar points upwards to the N terminus of Sf6 TSP with its
nonreducing end. Glu293 (chain C) and Asp247 (chain A) belong to
the binding site.
(B) Kinetics of hydrolysis of a
fluorescence-labeled dodecasaccharide (3 RU, 2 μM) with 0.36
μM Sf6 TSPΔN wild-type (closed triangles) and mutants D247N
(closed diamonds), E293Q (closed squares), E366Q (closed
circles) and D399N (open circles) at 15°C, as determined by
HPLC (Freiberg et al., 2003). See Table 1 for k[cat]/K[M] values
calculated from these data.
(C) An octasaccharide (2 RU)
modeled into the binding site with its reducing end reaching the
catalytic residues Asp399 and Glu366, which lie on different
chains, as indicated. Bridging water molecules are colored
purple.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2008,
16,
766-775)
copyright 2008.
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