1KFD: Crystal Structures Of The Klenow Fragment Of Dna Polymerase I Complexed With Deoxynucleoside Triphosphate And Pyrophosphate

Citation:
Abstract
Crystal structures of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli complexed with deoxynucleoside triphosphate (dNTP) or with pyrophosphate (PPi) determined to 3.9-A resolution by X-ray crystallography show these molecules binding within the cleft of the polymerase domain and surrounded by residues previously implicated in dNTP binding. The dNTP binds adjacent to the O-helix [Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G., & Steitz, T. A. (1985a) Nature 313, 762-766] with its triphosphate moiety anchored by three positively charged residues, Arg 754, Arg 682, and Lys 758, plus His 734 and Gln 708. The dNTP binding site observed in the crystal is consistent with the results of chemical modification including cross-linking and is also near many of the amino acid residues whose mutation affects catalysis [Polesky, A. H., Steitz, T. A., Grindley, N. D. F., & Joyce, C. M. (1990) J. Biol. Chem. 265, 14579-14591; Polesky, A. H., Dahlberg, M. E., Benkovic, S. J., Grindley, N. D. F., & Joyce, C. M. (1992) J. Biol. Chem. 267, 8417-8428]. However, we conclude that the position of at least the dNMP moiety of dNTP in the binary complex is not likely to be the same as in its catalytically relevant complex with primer-template DNA.
PDB ID: 1KFDDownload
MMDB ID: 56550
PDB Deposition Date: 1993/9/23
Updated in MMDB: 2007/10
Experimental Method:
x-ray diffraction
Resolution: 3.9  Å
Source Organism:
Similar Structures:
Biological Unit for 1KFD: monomeric; determined by author
Molecular Components in 1KFD
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase I Klenow Fragment(Gene symbol: polA)
Molecule annotation
Chemical (1 molecule)
1
1
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