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PDBsum entry 1bgx
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Complex (polymerase/inhibitor)
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PDB id
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1bgx
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Contents |
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828 a.a.
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210 a.a.
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209 a.a.
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* Residue conservation analysis
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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 taq DNA polymerase in complex with an inhibitory FAB: the FAB is directed against an intermediate in the helix-Coil dynamics of the enzyme.
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Authors
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R.Murali,
D.J.Sharkey,
J.L.Daiss,
H.M.Murthy.
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Ref.
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Proc Natl Acad Sci U S A, 1998,
95,
12562-12567.
[DOI no: ]
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PubMed id
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Abstract
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We report the crystal structure of Thermus aquaticus DNA polymerase I in complex
with an inhibitory Fab, TP7, directed against the native enzyme. Some of the
residues present in a helical conformation in the native enzyme have adopted a
gamma turn conformation in the complex. Taken together, structural information
that describes alteration of helical structure and solution studies that
demonstrate the ability of TP7 to inhibit 100% of the polymerase activity of the
enzyme suggest that the change in conformation is probably caused by trapping of
an intermediate in the helix-coil dynamics of this helix by the Fab. Antibodies
directed against modified helices in proteins have long been anticipated. The
present structure provides direct crystallographic evidence. The Fab binds
within the DNA binding cleft of the polymerase domain, interacting with several
residues that are used by the enzyme in binding the primer:template complex.
This result unequivocally corroborates inferences drawn from binding experiments
and modeling calculations that the inhibitory activity of this Fab is directly
attributable to its interference with DNA binding by the polymerase domain of
the enzyme. The combination of interactions made by the Fab residues in both the
polymerase and the vestigial editing nuclease domain of the enzyme reveal the
structural basis of its preference for binding to DNA polymerases of the Thermus
species. The orientation of the structure-specific nuclease domain with respect
to the polymerase domain is significantly different from that seen in other
structures of this polymerase. This reorientation does not appear to be
antibody-induced and implies remarkably high relative mobility between these two
domains.
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Figure 1.
Fig. 1. Electron density map with refined model
superimposed. Shown is a stereo representation of a 2F[o]  F[c] map,
contoured at 1.1  . Phases
were generated by removing residues 520-560 in TaqP and refining
the structure for 40 cycles with tight geometric restraints.
Final refined model for residues 540-550 in TaqP is
superimposed. All residues are labeled. The figure was made by
using SETOR (47).
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Figure 3.
Fig. 3. Overall View of the complex. C  ribbon
drawings of the pol domain (magenta), with the V-edit subdomain
colored orange, and light (green) and heavy chains (cyan) are
shown. Residues 540-550 in the helix are colored yellow. The
figure was made with GRASP (48).
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Secondary reference #1
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Title
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Structural studies on an inhibitory antibody against thermus aquaticus DNA polymerase suggest mode of inhibition.
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Authors
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R.Murali,
M.Helmer-Citterich,
D.J.Sharkey,
E.R.Scalice,
J.L.Daiss,
M.A.Sullivan,
H.M.Krishna murthy.
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Ref.
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Protein Eng, 1998,
11,
79-86.
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PubMed id
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