1EJ9

CRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX

Summary for 1EJ9

• Entry DOI: 10.2210/pdb1ej9/pdb
• Related: 1a31 1a35 1a36
• Descriptor: DNA (5'-D(*C*AP*AP*AP*AP*AP*GP*AP*CP*TP*CP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'), DNA (5'-D(*C*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*GP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'), DNA TOPOISOMERASE I, ... (4 entities in total)
• Functional Keywords: protein-dna complex, type i topoisomerase, human, isomerase-dna complex, isomerase/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus, nucleolus: P11387
• Total number of polymer chains: 3
• Total formula weight: 80669.03

Authors

Redinbo, M.R.,Champoux, J.J.,Hol, W.G. (deposition date: 2000-03-01, release date: 2000-08-03, Last modification date: 2024-02-07)

Primary citation

Redinbo, M.R.,Champoux, J.J.,Hol, W.G.
Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA.
Biochemistry, 39:6832-6840, 2000

PubMed Abstract: 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.

PubMed: 10841763
DOI: 10.1021/bi992690t

Experimental method

X-RAY DIFFRACTION (2.6 Å)