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PDBsum entry 1j59
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Gene regulation/DNA
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PDB id
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1j59
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Contents |
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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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Structure of the cap-Dna complex at 2.5 angstroms resolution: a complete picture of the protein-Dna interface.
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Authors
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G.Parkinson,
C.Wilson,
A.Gunasekera,
Y.W.Ebright,
R.H.Ebright,
R.E.Ebright,
H.M.Berman.
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Ref.
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J Mol Biol, 1996,
260,
395-408.
[DOI no: ]
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PubMed id
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Abstract
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The crystallographic structure of the CAP-DNA complex at 3.0 A resolution has
been reported previously. For technical reasons, the reported structure had been
determined using a gapped DNA molecule lacking two phosphates important for
CAP-DNA interaction. In this work, we report the crystallographic structure of
the CAP-DNA complex at 2.5 A resolution using a DNA molecule having all
phosphates important for CAP-DNA interaction. The present resolution permits
unambiguous identification of amino acid-base and amino acid-phosphate hydrogen
bonded contacts in the CAP-DNA complex. In addition, the present resolution
permits accurate definition of the kinked DNA conformation in the CAP-DNA
complex.
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Figure 1.
Figure 1. (a) DNA site for CAP. There are two conventions for numbering of positions within the DNA site for CAP:
convention 1 (Ebright et al., 1984a,b, 1987, 1989; Zhang & Ebright, 1990; Zhang et al., 1991; Gunasekera et al., 1992)
and convention 2 (Schultz et al., 1991). In this paper we use convention 1. (b) DNA molecule ``31-2'' used in the
previously reported structure of the CAP-DNA complex (Schultz et al., 1990, 1991). DNA molecule ``31-2'' contains
symmetry-related single-phosphate gaps between positions 9' and 10' and 13 and 14 (filled bars; see the text). (c) DNA
molecule ``31-2E'' used in the present structure of CAP-DNA complex. DNA molecule ``31-2E'' contains
symmetry-related single-phosphate gaps between positions 9 and 10 and 13' and 14' (filled bars; see the text).
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Figure 4.
Figure 4. Summary of CAP-DNA contacts in the structure of Schultz et al. (1991) (see footnote to p. 000). Contacts
in the half-complex A are from Schultz et al. (1991); contacts in the half-complex B are from the inspection of coordinates
(Brookhaven Protein Data Bank accession code 1cgp). (b) Summary of the CAP-DNA contacts in the present structure.
Contacts to the DNA phosphates missing in the structure of Schultz et al (1991) are in boldface.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
260,
395-408)
copyright 1996.
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