2FMS

DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site

Summary for 2FMS

• Entry DOI: 10.2210/pdb2fms/pdb
• Related: 2FMP 2FMQ
• Descriptor: 5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... (9 entities in total)
• Functional Keywords: nucleotidyl transferase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: P06746
• Total number of polymer chains: 4
• Total formula weight: 48395.43

Authors

Batra, V.K.,Beard, W.A.,Shock, D.D.,Krahn, J.M.,Pedersen, L.C.,Wilson, S.H. (deposition date: 2006-01-09, release date: 2006-04-25, Last modification date: 2023-08-30)

Primary citation

Batra, V.K.,Beard, W.A.,Shock, D.D.,Krahn, J.M.,Pedersen, L.C.,Wilson, S.H.
Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
Structure, 14:757-766, 2006

PubMed Abstract: 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.

PubMed: 16615916
DOI: 10.1016/j.str.2006.01.011

Experimental method

X-RAY DIFFRACTION (2 Å)