PDBsum entry 1pv4

Transcription/DNA

PDB id: 1pv4

Contents

Protein chains

408 a.a. *

358 a.a. *

Ligands

_DC-_DC ×5

Waters ×41

* Residue conservation analysis

PDB id:

1pv4

Name:

Transcription/DNA

Title:

X-ray crystal structure of the rho transcription termination factor in complex with single stranded DNA

Structure:

5'-d(p Cp C)-3'. Chain: g, h, j, k, l. Engineered: yes. Transcription termination factor rho. Chain: a, b, c, d, e, f. Fragment: bacterial transcription termination. Engineered: yes

Source:

Synthetic: yes. Other_details: rho transcription termination factor is an essential gene in bacteria. Escherichia coli. Organism_taxid: 562. Gene: rho. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

22mer (from PQS)

Resolution:

3.00Å R-factor: 0.271 R-free: 0.296

Authors:

E.Skordalakes,J.M.Berger

Key ref:

E.Skordalakes and J.M.Berger (2003). Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading. Cell, 114, 135-146. PubMed id: 12859904 DOI: 10.1016/S0092-8674(03)00512-9

Date:

26-Jun-03 Release date: 22-Jul-03

Protein chains

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

Seq: 419 a.a.

Struc: 408 a.a.

Protein chain

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

Seq: 419 a.a.

Struc: 358 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F: E.C.3.6.4.- - ?????

DOI no: 10.1016/S0092-8674(03)00512-9

Cell 114:135-146 (2003)

PubMed id: 12859904

Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading.

E.Skordalakes, J.M.Berger.

ABSTRACT

In bacteria, one of the major transcriptional termination mechanisms requires a RNA/DNA helicase known as the Rho factor. We have determined two structures of Rho complexed with nucleic acid recognition site mimics in both free and nucleotide bound states to 3.0 A resolution. Both structures show that Rho forms a hexameric ring in which two RNA binding sites--a primary one responsible for target mRNA recognition and a secondary one required for mRNA translocation and unwinding--point toward the center of the ring. Rather than forming a closed ring, the Rho hexamer is split open, resembling a "lock washer" in its global architecture. The distance between subunits at the opening is sufficiently wide (12 A) to accommodate single-stranded RNA. This open configuration most likely resembles a state poised to load onto mRNA and suggests how related ring-shaped enzymes may be breached to bind nucleic acids.

Selected figure(s)

Figure 3.
Figure 3. Rho RNA Binding Sites(A) Molecular surface (GRASP [Nicholls et al., 1991]) of the Rho hexamer. Primary RNA binding sites in the OB-fold of the N-terminal domain are colored cyan. Secondary (C-terminal) RNA binding sites in the ATPase domain are colored magenta. Nucleic acid bound at the primary RNA binding sites is shown as yellow rods. View is the same as in Figure 2B.(B) Schematic of the primary (N-terminal) RNA binding site configuration. The N- and C-terminal domains are colored green and red, respectively. Solid black lines represent the positions for the single-stranded nucleic acid, which binds across the primary RNA binding site and orients the 3′ end toward the hole of the ring. The broken black line shows the path needed to be traversed by nucleic acid between adjacent binding sites.(C) Rho's secondary RNA binding site. Stereo diagram of the Rho hexamer showing the location of the P loops (blue), the Q loops (magenta) and the R loops (green). View is from the “bottom,” rotated 180° from the perspective of Figure 2B.

Figure 5.
Figure 5. Schematic Model for Rho FunctionNumbers correspond to stages outlined in the text. Asterisks represent catalytic sites thought to be competent for ATP hydrolysis.

The above figures are reprinted by permission from Cell Press: Cell (2003, 114, 135-146) copyright 2003.

Figures were selected by an automated process.