PDBsum entry 2r92

Transferase/RNA

PDB id: 2r92

Contents

Protein chains

1422 a.a. *

1112 a.a. *

267 a.a. *

178 a.a. *

214 a.a. *

88 a.a. *

171 a.a. *

135 a.a. *

116 a.a. *

65 a.a. *

112 a.a. *

46 a.a. *

DNA/RNA

Metals

_MG

_ZN ×8

* Residue conservation analysis

PDB id:

2r92

Name:

Transferase/RNA

Title:

Elongation complex of RNA polymerase ii with artificial rdrp scaffold

Structure:

RNA (5'-r( Up Gp Cp Ap Up Ap Ap Ap Gp Ap Cp Cp Ap Gp Gp C)- 3'). Chain: p. Engineered: yes. RNA (5'- r( Cp Up Up Gp Ap Cp Gp Cp Cp Up Gp Gp Up Cp Ap Ap A)-3'). Chain: t. Engineered: yes. DNA-directed RNA polymerase ii subunit rpb1.

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932

Resolution:

3.80Å R-factor: 0.212 R-free: 0.246

Authors:

E.Lehmann,F.Brueckner,P.Cramer

Key ref:

E.Lehmann et al. (2007). Molecular basis of RNA-dependent RNA polymerase II activity. Nature, 450, 445-449. PubMed id: 18004386 DOI: 10.1038/nature06290

Date:

12-Sep-07 Release date: 27-Nov-07

Protein chain

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

Seq: 1733 a.a.

Struc: 1422 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: 267 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: 178 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: 88 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: 135 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: 116 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: 112 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 chains

A-G-A-C-C-A-G-G-C 9 bases

C-G-C-C-U-G-G-U-C-A 10 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/nature06290

Nature 450:445-449 (2007)

PubMed id: 18004386

Molecular basis of RNA-dependent RNA polymerase II activity.

E.Lehmann, F.Brueckner, P.Cramer.

ABSTRACT

RNA polymerase (Pol) II catalyses DNA-dependent RNA synthesis during gene transcription. There is, however, evidence that Pol II also possesses RNA-dependent RNA polymerase (RdRP) activity. Pol II can use a homopolymeric RNA template, can extend RNA by several nucleotides in the absence of DNA, and has been implicated in the replication of the RNA genomes of hepatitis delta virus (HDV) and plant viroids. Here we show the intrinsic RdRP activity of Pol II with only pure polymerase, an RNA template-product scaffold and nucleoside triphosphates (NTPs). Crystallography reveals the template-product duplex in the site occupied by the DNA-RNA hybrid during transcription. RdRP activity resides at the active site used during transcription, but it is slower and less processive than DNA-dependent activity. RdRP activity is also obtained with part of the HDV antigenome. The complex of transcription factor IIS (TFIIS) with Pol II can cleave one HDV strand, create a reactive stem-loop in the hybrid site, and extend the new RNA 3' end. Short RNA stem-loops with a 5' extension suffice for activity, but their growth to a critical length apparently impairs processivity. The RdRP activity of Pol II provides a missing link in molecular evolution, because it suggests that Pol II evolved from an ancient replicase that duplicated RNA genomes.

Selected figure(s)

Figure 2.
Figure 2: Crystal structure of a Pol II–RdRP complex. a, Ribbon model of Pol II (grey) with an initial, unbiased difference Fourier electron-density map (cyan, contoured at 2.2 ). The map was calculated from protein model phases. It reveals the RNA template–product duplex of scaffold RdRP-ss6 (Supplementary Fig. 2) in the active-centre cleft of Pol II. The bridge helix is in green. The catalytic metal ion A is depicted as a magenta sphere, and Zn^2+ ions as cyan spheres. The view is related to that in Fig. 1a by a 90° rotation around a vertical axis. b, Comparison of the RNA template–product duplex in the RdRP EC with the DNA–RNA hybrid duplex in the transcription EC^7. Protein structures were superimposed by fitting the active-site aspartate loops.

Figure 4.
Figure 4: Mechanism of HDV replication initiation. a, HDV-derived terminal stem-loops consisting of 5 or 6 bp enable templated incorporation of the next nucleotide(s). b, Pure Pol II–TFIIS complex cleaves the HDV antigenome terminal segment and elongates the newly formed 3' end on the addition of NTP. For cleavage, Pol II–scaffold complex (625 nM) was incubated with TFIIS (1.25 M) in transcription buffer for 60 min at 28 °C. For elongation of the cleavage product, the reaction mixture was incubated with 1 mM NTPs at 28 °C for 20 min. For lane 5, the cleavage reaction was stopped after 60 min ('Stop'). c, Difference electron density omit map for the 6-bp HDV stem-loop bound to the hybrid site of Pol II (calculated with protein phases only, contoured at 3.0 ). The disordered loop is indicated with a dashed line. The view is as in Fig. 2a. d, Superposition of the RNA template–product duplex in the HDV EC and the RdRP EC (Fig. 2) on the DNA–RNA hybrid duplex in the transcription EC^7. Protein structures were superimposed by fitting the active-site aspartate loops. e, Model of initial interaction of the HDV antigenome terminal segment with the Pol II–TFIIS complex. The stem-loop is placed in accordance with the crystal structure (c, d) and the downstream duplex in accordance with the location of the FC* RNA 3' stem. We predict that the HDV bulge passes the bridge helix and active site, where cleavage occurs.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 450, 445-449) copyright 2007.

Figures were selected by an automated process.