PDBsum entry 2b63

Transferase/RNA

PDB id: 2b63

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. *

115 a.a. *

46 a.a. *

DNA/RNA

Metals

_MG

_ZN ×8

* Residue conservation analysis

PDB id:

2b63

Name:

Transferase/RNA

Title:

Complete RNA polymerase ii-RNA inhibitor complex

Structure:

31-mer. Chain: r. Engineered: yes. DNA-directed RNA polymerase ii largest subunit. Chain: a. Synonym: RNA polymerase ii subunit 1, b220. DNA-directed RNA polymerase ii 140 kda polypeptide. Chain: b. Synonym: b150, RNA polymerase ii subunit 2.

Source:

Synthetic: yes. Other_details: synthetic oligonucleotide containing four 5-bromo- uridine (5bu) residues. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: rpb4. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

13mer (from PQS)

Resolution:

3.80Å R-factor: 0.252 R-free: 0.273

Authors:

H.Kettenberger,A.Eisenfuehr,F.Brueckner,M.Theis,M.Famulok,P.Cramer

Key ref:

H.Kettenberger et al. (2006). Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs. Nat Struct Mol Biol, 13, 44-48. PubMed id: 16341226 DOI: 10.1038/nsmb1032

Date:

30-Sep-05 Release date: 06-Dec-05

Protein chain

P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1733 a.a.

Struc: 1416 a.a.

Protein chain

P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1224 a.a.

Struc: 1112 a.a.

Protein chain

P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 318 a.a.

Struc: 266 a.a.

Protein chain

P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 221 a.a.

Struc: 177 a.a.

Protein chain

P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 214 a.a.

Protein chain

P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 155 a.a.

Struc: 84 a.a.

Protein chain

P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 171 a.a.

Struc: 171 a.a.

Protein chain

P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 146 a.a.

Struc: 133 a.a.

Protein chain

P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 122 a.a.

Struc: 119 a.a.

Protein chain

P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 70 a.a.

Struc: 65 a.a.

Protein chain

P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 120 a.a.

Struc: 115 a.a.

Protein chain

P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 70 a.a.

Struc: 46 a.a.

DNA/RNA chain

C-A-G-C-A-C-U-G-A-U-5BU-G-C-G-G-5BU-C-G-A-G-G-U-A-G-C-5BU-5BU-G-A-U-G 31 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/nsmb1032

Nat Struct Mol Biol 13:44-48 (2006)

PubMed id: 16341226

Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs.

H.Kettenberger, A.Eisenführ, F.Brueckner, M.Theis, M.Famulok, P.Cramer.

ABSTRACT

The noncoding RNA B2 and the RNA aptamer FC bind RNA polymerase (Pol) II and inhibit messenger RNA transcription initiation, but not elongation. We report the crystal structure of FC(*), the central part of FC RNA, bound to Pol II. FC(*) RNA forms a double stem-loop structure in the Pol II active center cleft. B2 RNA may bind similarly, as it competes with FC(*) RNA for Pol II interaction. Both RNA inhibitors apparently prevent the downstream DNA duplex and the template single strand from entering the cleft after DNA melting and thus interfere with open-complex formation. Elongation is not inhibited, as nucleic acids prebound in the cleft would exclude the RNA inhibitors. The structure also indicates that A-form RNA could interact with Pol II similarly to a B-form DNA promoter, as suggested for the bacterial transcription inhibitor 6S RNA.

Selected figure(s)

Figure 2.
Figure 2. FC^* RNA structure and analysis of Pol II contacts. (a) FC^* RNA atomic model and electron density maps. The unbiased difference Fourier electron density is shown as a grey net and is contoured at 4 (at lower contour level all nucleotides are covered by the density; data not shown). The bromine anomalous difference density map (insert) is shown as a red net at a contour level of 5.5 . The four bromine atoms and the phosphorus atoms are depicted as spheres. Throughout all figures, RNA is colored as follows: pink, 5' stem; red, 5' loop; orange, 3' stem; olive, 3' loop. The view is from the side (as defined in ref. 7). (b) Schematic of FC^* RNA and Pol II contacts. Four 5'-bromouracile residues used as markers are shown in red. Both terminal nucleotides are disordered. Pol II residues of the two large subunits within 4 Å of FC^* RNA are indicated, with residues of the Rpb2 subunit in italics, and interactions with bases, phosphate groups or sugar moieties are distinguished. Cyan, residues invariant between S. cerevisiae Pol I, II and III; green, conserved residues; continuous and dashed lines, potential base-pair interactions. (c) Mutants of FC^* RNA used for analysis of Pol II contacts. (d) Dissociation constants for the interaction of Pol II with the FC^* RNA mutants in c, as determined by in vitro binding assays.

Figure 4.
Figure 4. Model of RNA inhibition. (a) FC^* RNA and nucleic acids in the Pol II elongation complex bind overlapping sites. The Pol II-FC^* RNA complex structure was superimposed on the structure of the complete Pol II elongation complex9. Phosphate groups that occupy similar locations are labeled. The view is from the side (as defined in ref. 7). (b) Competition binding analysis suggests that FC^* RNA and B2 RNA bind overlapping sites. Pol II complexes with radioactively labeled FC^* RNA (top) or B2 RNA (bottom) were challenged with increasing concentrations of unlabeled competitor RNA as indicated. Mutant 9 was used as a negative control (Fig. 1c). See Methods for details. (c) Model for inhibition of open-complex formation by FC^* RNA. The view is from the side^7. The upstream region of the DNA promoter was placed on Pol II on the basis of its location in the bacterial RNA polymerase-promoter complex13 and was extrapolated in the downstream direction. The downstream region of promoter DNA and the template strand in the bubble region of the open complex were modeled according to the complete Pol II elongation complex9. FC^* RNA is shown as a molecular surface.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 44-48) copyright 2006.

Figures were selected by an automated process.