PDBsum entry 2rf4

Transferase

PDB id: 2rf4

Contents

Protein chains

174 a.a. *

61 a.a. *

* Residue conservation analysis

PDB id:

2rf4

Name:

Transferase

Title:

Crystal structure of the RNA polymerase i subcomplex a14/43

Structure:

DNA-directed RNA polymerase i subunit rpa4. Chain: a, c, e. Synonym: DNA-directed DNA-dependent RNA polymerase 36 kda polypeptide, a43. Engineered: yes. DNA-directed RNA polymerase i subunit rpa4. Chain: b, d, f. Synonym: DNA-directed RNA polymerase i 14 kda polypeptide, a14. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: rpa43, rrn12. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

3.10Å R-factor: 0.252 R-free: 0.285

Authors:

S.R.Geiger,C.D.Kuhn,P.Cramer

Key ref:

C.D.Kuhn et al. (2007). Functional architecture of RNA polymerase I. Cell, 131, 1260-1272. PubMed id: 18160037 DOI: 10.1016/j.cell.2007.10.051

Date:

28-Sep-07 Release date: 15-Jan-08

Protein chains

P46669  (RPA43_YEAST) -  DNA-directed RNA polymerase I subunit RPA43 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 326 a.a.

Struc: 174 a.a.

Protein chains

P50106  (RPA14_YEAST) -  DNA-directed RNA polymerase I subunit RPA14 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 137 a.a.

Struc: 61 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F: 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: 10.1016/j.cell.2007.10.051

Cell 131:1260-1272 (2007)

PubMed id: 18160037

Functional architecture of RNA polymerase I.

C.D.Kuhn, S.R.Geiger, S.Baumli, M.Gartmann, J.Gerber, S.Jennebach, T.Mielke, H.Tschochner, R.Beckmann, P.Cramer.

ABSTRACT

Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming.

Selected figure(s)

Figure 2.
Figure 2. Model and EM Features of the Pol I Core
(A) Placement of the Pol II ten-subunit core structure (Armache et al., 2005) (gray) into the EM density (blue). The foot was deleted, and subunits Rpb5, Rpb8, and Rpb9 are highlighted in magenta, green, and orange, respectively. The clamp has been fitted as a separate rigid body.
(B) Fit of the common subunits Rpb5 and Rpb8 to the EM map, and density for the core subunit A12.2 (the Pol II homolog Rpb9 is shown as a ribbon model).
(C) Pol II structure-guided sequence alignment of the five Pol I subunits with homologs in Pol II (compare Table 1). The domain organization of Pol II subunits Rpb1, Rpb2, Rpb3, Rpb11, and Rpb9 is shown as diagrams (Cramer et al., 2001). Insertions and deletions exceeding five amino acid residues are indicated. Conserved folds are indicated by orange highlighting of the bar above the diagrams. For details see Figure S1.
(D) View of the core Pol II structure (Cramer et al., 2001) from the side, with domains depicted in (E) highlighted.
(E) Pol I-specific structural elements. Fitted Pol II elements are shown as ribbon models. Insertions and deletions explaining the EM density are named according to (C). The clamp head is in light red and the clamp core in red. The dock and foot domains are in beige and blue, respectively, and Rpb3, Rpb10, and Rpb11 are in red, dark blue, and in yellow, respectively. Zinc ions are depicted as marine spheres.

Figure 5.
Figure 5. Intrinsic RNA Cleavage Activity and Functional Architecture of Pol I
(A) DNA-RNA hybrid scaffold used in cleavage assays.
(B) Comparison of RNA cleavage by Pol I variants with Pol II and the Pol II-TFIIS complex. Pol I mainly removed four nucleotides from the RNA, consistent with binding of the terminal hybrid base pair to the nucleotide insertion site (+1), extrusion of the RNA 3′ overhang into the polymerase pore and cleavage of the phosphodiester bond between nucleotides at positions −1 and +1 (Figure 5A). The Pol II-TFIIS complex removed three or four nucleotides, indicating that a mixture of complexes was present with the terminal hybrid base pair occupying either position −1 or +1.
(C) pH dependence of pol I cleavage activity.
(D) Elongation activity of the Pol I variant A12.2ΔC.
(E) Hybrid structure and functional architecture of Pol I. The EM envelope is shown as a blue line, the Pol I core ribbon model in gray with Rpb9 (A12.2) highlighted in orange, and the A14/43 crystal structure in red/blue. The window shows a cut-away view of the active center containing a modeled DNA-RNA hybrid. Red dashes indicate the RNA 3′ end extruded into the pore.

The above figures are reprinted by permission from Cell Press: Cell (2007, 131, 1260-1272) copyright 2007.

Figures were selected by an automated process.