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PDBsum entry 1ej9
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Isomerase/DNA
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PDB id
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1ej9
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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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Novel insights into catalytic mechanism from a crystal structure of human topoisomerase i in complex with DNA.
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Authors
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M.R.Redinbo,
J.J.Champoux,
W.G.Hol.
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Ref.
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Biochemistry, 2000,
39,
6832-6840.
[DOI no: ]
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PubMed id
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Abstract
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Human topoisomerase I helps to control the level of DNA supercoiling in cells
and is vital for numerous DNA metabolic events, including replication,
transcription, and recombination. The 2.6 A crystal structure of human
topoisomerase I in noncovalent complex with a DNA duplex containing a cytosine
at the -1 position of the scissile strand rather than the favored thymine is
reported. The hydrogen bond between the O2 position of this -1 base and the
epsilon-amino of the conserved Lys-532 residue, the only base-specific contact
observed previously in the human topoisomerase I-DNA interaction, is maintained
in this complex. Several unique features of this structure, however, have
implications for the DNA-binding and active-site mechanisms of the enzyme.
First, the ends of the DNA duplex were observed to shift by up to 5.4 A
perpendicular to the DNA helical axis relative to structures reported
previously, suggesting a novel degree of plasticity in the interaction between
human topoisomerase I and its DNA substrate. Second, 12 additional residues at
the NH(2) terminus of the protein (Trp-203-Gly-214) could be built in this
structure, and they were found to pack against the putative hinge region
implicated in the clamping of the enzyme around duplex DNA. Third, a water
molecule was observed adjacent to the scissile phosphate and the active-site
residues; the potential specific base character of this solvent molecule in the
active-site mechanism of the enzyme is discussed. Fourth, the scissile phosphate
group was found to be rotated by 75 degrees, bringing Lys-532 into
hydrogen-bonding distance of one of the nonbridging phosphate oxygens. This
orientation of the scissile phosphate group implicates Lys-532 as a fifth
active-site residue, and also mimics the orientation observed for the
3'-phosphotyrosine linkage in the covalent human topoisomerase I-DNA complex
structure. The implications of these structural features for the mechanism of
the enzyme are discussed, including the potential requirement for a rotation of
the scissile phosphate group during DNA strand cleavage and covalent attachment.
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