PDBsum entry 1a8v

Transcription termination

PDB id: 1a8v

Contents

Protein chains

115 a.a. *

Metals

_CU ×2

Waters ×88

* Residue conservation analysis

PDB id:

1a8v

Name:

Transcription termination

Title:

Structure of the RNA-binding domain of the rho transcription terminator

Structure:

Transcription termination factor rho. Chain: a, b. Fragment: RNA-binding domain. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: dh5-alpha. Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.193 R-free: 0.261

Authors:

D.Fass,C.Bogden,J.M.Berger

Key ref:

C.E.Bogden et al. (1999). The structural basis for terminator recognition by the Rho transcription termination factor. Mol Cell, 3, 487-493. PubMed id: 10230401 DOI: 10.1016/S1097-2765(00)80476-1

Date:

28-Mar-98 Release date: 04-May-99

Protein chains

P0AG30  (RHO_ECOLI) -  Transcription termination factor Rho from Escherichia coli (strain K12)

Seq: 419 a.a.

Struc: 115 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.4.- - ?????

DOI no: 10.1016/S1097-2765(00)80476-1

Mol Cell 3:487-493 (1999)

PubMed id: 10230401

The structural basis for terminator recognition by the Rho transcription termination factor.

C.E.Bogden, D.Fass, N.Bergman, M.D.Nichols, J.M.Berger.

ABSTRACT

The E. coli Rho protein disengages newly transcribed RNA from its DNA template, helping terminate certain transcripts. We have determined the X-ray crystal structure of the RNA-binding domain of Rho complexed to an RNA ligand. Filters that screen both ligand size and chemical functionality line the primary nucleic acid-binding site, imparting sequence specificity to a generic single-stranded nucleic acid-binding fold and explaining the preference of Rho for cytosine-rich RNA. The crystal packing reveals two Rho domain protomers bound to a single RNA with a single base spacer, suggesting that the strong RNA-binding sites of Rho may arise from pairing of RNA-binding modules. Dimerization of symmetric subunits on an asymmetric ligand is developed as a model for allosteric control in the action of the intact Rho hexamer.

Selected figure(s)

Figure 1.
Figure 1. Structure of Rho13N Bound to RNA(a) Experimental electron density map superposed on a ball-and-stick model of the refined RNA. The map was generated using phases from the 3-fold-averaged poly-serine molecular replacement solution and the observed structure factors. Gold contours are at 1.0 σ and cyan at 2.5 σ.(b) Refined 2F[o] − F[c], model-phased map of the same region. Gold contours are at 1.3 σ.(c) Front view of the secondary structure of Rho13N monomer (green) shown with bound oligoribocytidine (ball-and-stick) in the OB-fold cleft. The cleft is formed on the surface of strands β2 and β3, with the β1–β2 and β4–β5 loops forming parts of the lower and upper walls, respectively. Helices and strands are labeled.(d) View as in (c), rotated 90° about the vertical axis ([a] and [b] generated by BOBSCRIPT and RASTER3D [[40 and 22]]; (c) and (d) generated by RIBBONS [ [12]]).

Figure 2.
Figure 2. Specific Interactions of Rho13N with Its Target RNA(a) The RNA moiety (blue sticks) is shown on a surface representation of the Rho13N C-terminal subdomain. The C[α] path of Rho13N is marked by a gold coil, while residues and atoms that interact directly with the RNA are colored black and labeled.(b) Stereo view of the environment around the first RNA cytosine. A Van der Waals dot surface is drawn about the protein atoms. Hydrogen bonds are indicated by dashed lines.(c) Stereo view of the Watson/Crick-like recognition of the hydrogen bond donor/acceptor groups of the second RNA cytosine by Arg-66 and Asp-78; the cytidine base stacks on the ring of Phe-64. The orientation of these side chains with respect to the cytosine base is tilted slightly, analogous to a “propeller twist.”(d) Stereo view of a DNA C·G base pair (from PDB accession number 126D [[29]]); the cytosine base is stacked on the ring of a second cytosine (figure generated by RIBBONS [ [12]]).

The above figures are reprinted by permission from Cell Press: Mol Cell (1999, 3, 487-493) copyright 1999.

Figures were selected by an automated process.