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PDBsum entry 1twa

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Transcription PDB id
1twa
Jmol
Contents
Protein chains
1352 a.a.
1091 a.a.
266 a.a.
215 a.a.
83 a.a.
133 a.a.
121 a.a.
64 a.a.
114 a.a.
46 a.a.
Ligands
ATP
Metals
_MN ×2
_ZN ×8

References listed in PDB file
Key reference
Title Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase ii active center.
Authors K.D.Westover, D.A.Bushnell, R.D.Kornberg.
Ref. Cell, 2004, 119, 481-489. [DOI no: 10.1016/j.cell.2004.10.016]
PubMed id 15537538
Abstract
Binding of a ribonucleoside triphosphate to an RNA polymerase II transcribing complex, with base pairing to the template DNA, was revealed by X-ray crystallography. Binding of a mismatched nucleoside triphosphate was also detected, but in an adjacent site, inverted with respect to the correctly paired nucleotide. The results are consistent with a two-step mechanism of nucleotide selection, with initial binding to an entry (E) site beneath the active center in an inverted orientation, followed by rotation into the nucleotide addition (A) site for pairing with the template DNA. This mechanism is unrelated to that of single subunit RNA polymerases and so defines a new paradigm for the large, multisubunit enzymes. Additional findings from these studies include a third nucleotide binding site that may define the length of backtracked RNA; DNA double helix unwinding in advance of the polymerase active center; and extension of the diffraction limit of RNA polymerase II crystals to 2.3 A.
Figure 2.
Figure 2. Downstream End of the DNA-RNA Hybrid in Transcribing Complex Structures, Showing Occupancy of the A and E Sites(A) Transcribing complex with matched NTP (UTP) in the A site.(B) Transcribing complex with mismatched NTP (ATP) in the E site. Views are the same as in Figure 1. DNA is blue, RNA is red, and NTPs are in yellow. Mg ions are shown as magenta spheres.
Figure 5.
Figure 5. Substrate Entry to Active Center Regions of Single and Multisubunit PolymerasesSolvent-accessible surfaces for transcribing complexes of (A) pol II and (B) T7 RNA polymerase (PDB 1H38) are shown, in a “front” view of pol II (Cramer et al., 2000) and corresponding view of the T7 enzyme (aligned on the sugar-phosphate backbone of the DNA-RNA hybrid) (Tahirov et al., 2002), with the front portion of the proteins cut away to reveal the DNA-RNA hybrid (DNA blue, RNA red). A mismatched NTP bound to pol II as in Figure 2D is shown in pink. The direction of substrate entry to the active center is indicated by a black arrow.
The above figures are reprinted by permission from Cell Press: Cell (2004, 119, 481-489) copyright 2004.
PROCHECK
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