2fms
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DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site
OverviewOverview
The molecular details of the nucleotidyl transferase reaction have, remained speculative, as strategies to trap catalytic intermediates for, structure determination utilize substrates lacking the primer terminus, 3'-OH and catalytic Mg2+, resulting in an incomplete and distorted active, site geometry. Since the geometric arrangement of these essential atoms, will impact chemistry, structural insight into fidelity strategies has, been hampered. Here, we present a crystal structure of a precatalytic, complex of a DNA polymerase with bound substrates that include the primer, 3'-OH and catalytic Mg2+. This catalytic intermediate was trapped with a, nonhydrolyzable deoxynucleotide analog. Comparison with two new structures, of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is described., These structures provide direct evidence that both atoms are required to, achieve a proper geometry necessary for an in-line nucleophilic attack of, O3' on the alphaP of the incoming nucleotide.
About this StructureAbout this Structure
2FMS is a Single protein structure of sequence from Homo sapiens with MG, NA, CL and DUP as ligands. Full crystallographic information is available from OCA.
ReferenceReference
Magnesium-induced assembly of a complete DNA polymerase catalytic complex., Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH, Structure. 2006 Apr;14(4):757-66. PMID:16615916
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