PDBsum entry: 1i6v

Transcription

PDB id: 1i6v

Contents

Protein chains

224 a.a. *

1113 a.a. *

1174 a.a. *

98 a.a. *

Ligands

RFP

Metals

_ZN

_MG

* Residue conservation analysis

PDB id:

1i6v

Name:

Transcription

Title:

Thermus aquaticus core RNA polymerase-rifampicin complex

Structure:

DNA-directed RNA polymerase. Chain: a, b. Fragment: alpha subunit. DNA-directed RNA polymerase. Chain: c. Fragment: beta subunit. DNA-directed RNA polymerase. Chain: d. Fragment: beta-prime subunit.

Source:

Thermus aquaticus. Organism_taxid: 271. Organism_taxid: 271

Biol. unit:

Pentamer (from PQS)

Resolution:

3.30Å R-factor: 0.276 R-free: 0.359

Authors:

E.A.Campbell,N.Korzheva,A.Mustaev,K.Murakami,A.Goldfarb, S.A.Darst

Key ref:

E.A.Campbell et al. (2001). Structural mechanism for rifampicin inhibition of bacterial rna polymerase. Cell, 104, 901-912. PubMed id: 11290327 DOI: 10.1016/S0092-8674(01)00286-0

Date:

05-Mar-01 Release date: 18-Apr-01

Protein chains

Q9KWU8  (RPOA_THEAQ) -  DNA-directed RNA polymerase subunit alpha

Seq: 314 a.a.

Struc: 224 a.a.*

Protein chain

Q9KWU7  (RPOB_THEAQ) -  DNA-directed RNA polymerase subunit beta

Seq: 1119 a.a.

Struc: 1113 a.a.*

Protein chain

Q9KWU6  (RPOC_THEAQ) -  DNA-directed RNA polymerase subunit beta'

Seq: 1524 a.a.

Struc: 1174 a.a.*

Protein chain

Q9EVV4  (RPOZ_THEAQ) -  DNA-directed RNA polymerase subunit omega

Seq: 99 a.a.

Struc: 98 a.a.

* PDB and UniProt seqs differ at 48 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E: 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 

• Cellular component: RNA polymerase complex (1 term)
• Biological process: DNA repair (3 terms)
• Biochemical function: transferase activity (6 terms)

reference

DOI no: 10.1016/S0092-8674(01)00286-0

Cell 104:901-912 (2001)

PubMed id: 11290327

Structural mechanism for rifampicin inhibition of bacterial rna polymerase.

E.A.Campbell, N.Korzheva, A.Mustaev, K.Murakami, S.Nair, A.Goldfarb, S.A.Darst.

ABSTRACT

Rifampicin (Rif) is one of the most potent and broad spectrum antibiotics against bacterial pathogens and is a key component of anti-tuberculosis therapy, stemming from its inhibition of the bacterial RNA polymerase (RNAP). We determined the crystal structure of Thermus aquaticus core RNAP complexed with Rif. The inhibitor binds in a pocket of the RNAP beta subunit deep within the DNA/RNA channel, but more than 12 A away from the active site. The structure, combined with biochemical results, explains the effects of Rif on RNAP function and indicates that the inhibitor acts by directly blocking the path of the elongating RNA when the transcript becomes 2 to 3 nt in length.

Selected figure(s)

Figure 4.
Figure 4. Detailed Interactions of Rif with RNAP(a) Stereo view of the Taq RNAP Rif binding pocket complexed with Rif, generated using RIBBONS (Carson, 1991), showing residues that interact directly with the inhibitor. The view is from the top of the RNAP in Figure 3b, above the β subunit, looking down through β to the Rif, but with obscuring parts of β removed. The backbone of the β subunit is shown as a cyan ribbon. Side chains (and backbone atoms of F394) of residues within 4 Å of Rif are shown. Carbon atoms are orange (Rif), magenta (three residues substituted in M. tuberculosis Rif^R clinical isolates with high frequency, see Figure 1), or yellow; oxygen atoms are red; nitrogen atoms are blue. Potential hydrogen bonds between protein atoms and Rif are shown as dashed lines.(b) Schematic drawing of RNAP β subunit interactions with Rif, modified from LIGPLOT (Wallace et al., 1995). Residues forming van der Waals interactions are indicated, those participating in hydrogen bonds are shown in a ball-and-stick representation, with hydrogen bonds depicted as dashed lines. Carbon atoms of the protein are black, while carbon atoms of Rif are orange. Oxygen atoms are red and nitrogen atoms are blue

Figure 6.
Figure 6. Mechanism of RNAP Inhibition by Rif(a) The RNAP active site Mg^2+ (magenta sphere) and the 9 bp RNA/DNA hybrid (from +1 to −8) from a model of the ternary elongation complex (Korzheva et al., 2000) are shown. The RNAP itself and the rest of the nucleic acids are omitted for clarity. The incoming nucleotide substrate at the +1 position is colored green, the −1 and −2 positions, which can be accommodated in the presence of Rif, are colored yellow. The RNA further upstream (−3 to −8), which cannot be accommodated in the presence of Rif, is colored pink. The template strand of the DNA is colored gray. Also shown is a CPK representation of Rif as it would be positioned in its binding site on the β subunit (carbon atoms, orange; oxygen, red; nitrogen, blue). The Rif is partially transparent, illustrating the RNA nucleotides at −3 to −5 that sterically clash. Generated using GRASP (Nicholls et al., 1991).(b) The structure of the minimal scaffold systems with RNA lengths from 3–7 nt (labeled above the RNA chain; Korzheva et al., 2000). The results are presented below as autoradiographs of the radioactive RNAs produced by E. coli (lanes 1–15) or Taq (lanes 16–30) core RNAPs transcribing the minimal scaffolds with the indicated lengths of RNA (“X =”) and analyzed on a 23% polyacrylamide gel. Lanes 1–10 and 16–25 demonstrate the effect of Rif inhibition of transcription when it was bound by RNAP either before (lanes 1–5 and 16–20) or after (lanes 6–10 and lanes 21–25) addition of the scaffold. Lanes 11–15 and 26–30 show elongation of the same scaffolds in the absence of Rif. The RNA with the critical length of 3 nt, which cannot be elongated by E. coli RNAP in the presence of Rif regardless of the order of Rif and scaffold addition (lanes 1 and 6), is colored red. The RNAs of 4–7 nt (colored green) were extended by E. coli RNAP when added before Rif (lanes 6–10)

The above figures are reprinted by permission from Cell Press: Cell (2001, 104, 901-912) copyright 2001.

Figures were selected by the author.