PDBsum entry 1y77

Transcription,transferase/DNA-RNA hybrid

PDB id: 1y77

Contents

Protein chains

1416 a.a.

1112 a.a.

266 a.a.

177 a.a.

214 a.a.

84 a.a.

171 a.a.

133 a.a.

119 a.a.

65 a.a.

114 a.a.

46 a.a.

DNA/RNA

Ligands

G2P

Metals

_MG

_ZN ×8

References listed in PDB file

Key reference

Title

Complete RNA polymerase ii elongation complex structure and its interactions with ntp and tfiis.

Authors

H.Kettenberger, K.J.Armache, P.Cramer.

Ref.

Mol Cell, 2004, 16, 955-965. [DOI no: 10.1016/j.molcel.2004.11.040]

PubMed id

15610738

Abstract

The crystal structure of the complete 12 subunit RNA polymerase (pol) II bound to a transcription bubble and product RNA reveals incoming template and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three nucleotides each of separating DNA and RNA. The complex adopts the posttranslocation state and accommodates a cocrystallized nucleoside triphosphate (NTP) substrate. The NTP binds in the active site pore at a position to interact with a DNA template base. Residues surrounding the NTP are conserved in all cellular RNA polymerases, suggesting a universal mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand separation may be explained by pol II-induced duplex distortions. Four protein loops partition the active center cleft, contribute to embedding the hybrid, prevent strand reassociation, and create an RNA exit tunnel. Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling.

Figure 4.
Figure 4. Conservation and Compartmentalization of the Polymerase Cleft(A) Overall structure of the pol II-bubble-RNA complex. The complete pol II is shown as a molecular surface, and nucleic acid backbones are drawn as ribbons. The view corresponds to the front view (Cramer et al. 2000 and Cramer et al. 2001). A dashed line indicates the slice plane used to create the views in (C).(B) Top view of the model in (A). Pol II loops are outlined that partition the enzyme cleft. During transcription elongation, DNA enters from the right. Previously proposed RNA exit grooves are labeled 1 and 2.(C) Conservation of nucleic-acid interaction surfaces. The model in (A) was intersected along the plane indicated in (A), and the resulting halves were rotated by 90° around a vertical axis in opposite directions. The molecular surface of residues within 8 Å distance from nucleic acids is colored in beige. Residues that are invariant and conserved between pol I, II, and III are highlighted in dark and light green, respectively. Pol II elements that contact nucleic acids and partition the enzyme cleft are outlined.

Figure 6.
Figure 6. TFIIS-Induced RNA RealignmentSelected elements in the pol II active center that move upon TFIIS binding are shown. The bridge helix, DNA, and RNA in the pol II-bubble-RNA-TFIIS complex are in green, blue, and red, respectively. The TFIIS hairpin is in orange with the two acidic functionally essential and invariant residues in green. Nucleic acids in the pol II-bubble-RNA complex structure after superposition of residues in the active site aspartate loop or in switch 2 are shown in beige and gray, respectively. Switch 2 moves slightly upon TFIIS binding (Kettenberger et al., 2003), explaining the difference in the two superpositions.

The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 16, 955-965) copyright 2004.