A unified DNA- and dNTP-binding mode for DNA polymerases.
Crystal structures of various DNA polymerases show a common structural topology that resembles a right hand and has distinct finger, palm and thumb subdomains. Early models of the klenow fragment (KF) of Escherichia coli polymerase I showed DNA entering a large cleft that faces the palm subdomain where the catalytic site is situated1,2. However, subsequent resolution of the structures of HIV-1 reverse transcriptase, KF and polymerase beta (pol beta) bound to DNA3-5 yielded conflicting data that suggested a different orientation for DNA bound to pol beta compared with DNA bound to other polymerases. The debate, on the correct orientation of the template-primer DNA, that followed failed to reach a consensus. Using an alternative superposition scheme, we now provide convincing evidence for a common DNA-binding mode that is applicable to all polymerases, including pol beta.
Singh
K
K
Dept of Biochemistry and Molecular Biology, UMD-New Jersey Medical School, Newark 07103, USA.
Modak
M J
MJ
D001665:Binding Sites; D004247:DNA / Q000378:metabolism; D004256:DNA Polymerase I / Q000737:chemistry / Q000378:metabolism; D019951:DNA Polymerase beta / Q000737:chemistry / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000378:metabolism*; D054303:HIV Reverse Transcriptase / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D019914:Taq Polymerase / Q000737:chemistry / Q000378:metabolism
D004247:DNA; D019914:Taq Polymerase; D054303:HIV Reverse Transcriptase; D004256:DNA Polymerase I; D019951:DNA Polymerase beta; D004259:DNA-Directed DNA Polymerase