PDBsum entry: 1go3

Transferase

PDB id: 1go3

Contents

Protein chains

177 a.a. *

107 a.a. *

Waters ×328

* Residue conservation analysis

PDB id:

1go3

Name:

Transferase

Title:

Structure of an archeal homolog of the eukaryotic RNA polymerase ii rpb4/rpb7 complex

Structure:

DNA-directed RNA polymerase subunit e. Chain: e, m. Engineered: yes. DNA-directed RNA polymerase subunit f. Chain: f, n. Engineered: yes

Source:

Methanococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3. Other_details: co-expressed using a bicistrionic expression strategy. Expression strategy

Biol. unit:

Dimer (from PDB file)

Resolution:

1.75Å R-factor: 0.217 R-free: 0.238

Authors:

F.Todone,P.Brick,F.Werner,R.O.J.Weinzierl,S.Onesti

Key ref:

F.Todone et al. (2001). Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. Mol Cell, 8, 1137-1143. PubMed id: 11741548 DOI: 10.1016/S1097-2765(01)00379-3

Date:

17-Oct-01 Release date: 07-Dec-01

Protein chains

Q57840  (RPOE1_METJA) -  DNA-directed RNA polymerase subunit E'

Seq: 187 a.a.

Struc: 177 a.a.

Protein chains

Q60351  (Y039_METJA) -  Uncharacterized protein MJ0039

Seq: 115 a.a.

Struc: 107 a.a.

Enzyme reactions

• Enzyme class: Chains E, M: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)

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

 Gene Ontology (GO) functional annotation 

• Biological process: cellular metabolic process (2 terms)
• Biochemical function: catalytic activity (7 terms)

reference

DOI no: 10.1016/S1097-2765(01)00379-3

Mol Cell 8:1137-1143 (2001)

PubMed id: 11741548

Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex.

F.Todone, P.Brick, F.Werner, R.O.Weinzierl, S.Onesti.

ABSTRACT

The eukaryotic subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core and constitute the only two components of the enzyme for which no structural information is available. We have determined the crystal structure of the complex between the Methanococcus jannaschii subunits E and F, the archaeal homologs of RPB7 and RPB4. Subunit E has an elongated two-domain structure and contains two potential RNA binding motifs, while the smaller F subunit wraps around one side of subunit E, at the interface between the two domains. We propose a model for the interaction between RPB4/RPB7 and the core RNA polymerase in which the RNA binding face of RPB7 is positioned to interact with the nascent RNA transcript.

Selected figure(s)

Figure 3.
Figure 3. Surface Electrostatic PotentialMapping of the electrostatic potential on the surface of the E/F complex, with negative charges shown in red and positive charges in blue. On the left-hand side of the picture, the complex is shown in the same orientation as in Figure 2A (front), while on the right-hand side it is rotated by 180° around a vertical axis (back). The heterodimer shows a strikingly asymmetric charge distribution, with one side of the complex (particularly subunit F) highly negatively charged.

Figure 4.
Figure 4. Proposed Model for the Interaction of RPB4/RPB7 with the RNA Polymerase CoreA schematic representation of the RNAP[II] 10 subunit core is shown (viewed in a similar orientation as the side view in Figures 3 and 6D of Cramer et al. (2000), with RPB5 shown in red and the mobile clamp, which closes onto the active side cleft upon nucleic acid binding, shown in green. The predicted exit path for the nascent RNA transcript is shown as a dashed line, and the proposed location of the heterodimer shown as a blue circle. The structure of the E/F complex is shown rotated by approximately 130° around a vertical axis with respect to the orientation used in Figure 2A. The position and orientation of the heterodimer is consistent with a wide range of structural and biological results, including low-resolution studies on 2D crystals and the positioning of the S1 motif binding face onto the nascent RNA transcript. The negatively charged surface of the F subunit is positioned on the outside, the insertion in the yeast RPB4 structure can be easily accommodated, and RPB7 plays the main role in the interaction, in agreement with the biochemical and genetic results.

The above figures are reprinted by permission from Cell Press: Mol Cell (2001, 8, 1137-1143) copyright 2001.

Figures were selected by an automated process.