2VAN
Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses
Summary for 2VAN
| Entry DOI | 10.2210/pdb2van/pdb |
| Related | 1BNO 1BNP 1BPB 1BPD 1BPE 1DK2 1DK3 1HUO 1HUZ 1JN3 1NOM 1RPL 1ZQU 1ZQV 1ZQW 1ZQX 1ZQY 1ZQZ 2BPC 2BPF 2BPG |
| Descriptor | DNA POLYMERSE BETA (2 entities in total) |
| Functional Keywords | nucleotidyltransferase, dna-directed dna polymerase, lyase, nucleus, dna damage, dna synthesis, dna replication, dna repair, transferase, dna-binding, metal-binding |
| Biological source | RATTUS NORVEGICUS (NORWAY RAT) |
| Cellular location | Nucleus: P06766 |
| Total number of polymer chains | 1 |
| Total formula weight | 28391.02 |
| Authors | |
| Primary citation | Tang, K.,Niebuhr, M.,Tung, C.,Chan, H.,Chou, C.,Tsai, M. Mismatched Dntp Incorporation by DNA Polymerase Beta Does not Proceed Via Globally Different Conformational Pathways. Nucleic Acids Res., 36:2948-, 2008 Cited by PubMed Abstract: Understanding how DNA polymerases control fidelity requires elucidation of the mechanisms of matched and mismatched dNTP incorporations. Little is known about the latter because mismatched complexes do not crystallize readily. In this report, we employed small-angle X-ray scattering (SAXS) and structural modeling to probe the conformations of different intermediate states of mammalian DNA polymerase beta (Pol beta) in its wild-type and an error-prone variant, I260Q. Our structural results indicate that the mismatched ternary complex lies in-between the open and the closed forms, but more closely resembles the open form for WT and the closed form for I260Q. On the basis of molecular modeling, this over-stabilization of mismatched ternary complex of I260Q is likely caused by formation of a hydrogen bonding network between the side chains of Gln(260), Tyr(296), Glu(295) and Arg(258), freeing up Asp(192) to coordinate MgdNTP. These results argue against recent reports suggesting that mismatched dNTP incorporations follow a conformational path distinctly different from that of matched dNTP incorporation, or that its conformational closing is a major contributor to fidelity. PubMed: 18385153DOI: 10.1093/NAR/GKN138 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.1 Å) |
Structure validation
Download full validation report
