PDBsum entry: 1xs9

Transcription/DNA

PDB id: 1xs9

Contents

Protein chains

129 a.a. *

81 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1xs9

Name:

Transcription/DNA

Title:

A model of the ternary complex formed between mara, the alpha-ctd of RNA polymerase and DNA

Structure:

Multiple antibiotic resistance protein mara. Chain: a. Engineered: yes. 5'- d(p Gp Ap Tp Tp Tp Ap Gp Cp Ap Ap Ap Ap Cp Gp Tp Gp Gp Cp A p T)-3'. Chain: b. Fragment: promoter region. Engineered: yes.

Source:

Escherichia coli. Organism_taxid: 562. Gene: mara. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Gene: rpoa, pez, phs, sez.

NMR struc:

1 models

Authors:

B.Dangi,A.M.Gronenborn,J.L.Rosner,R.G.Martin

Key ref:

B.Dangi et al. (2004). Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA. Mol Microbiol, 54, 45-59. PubMed id: 15458404 DOI: 10.1111/j.1365-2958.2004.04250.x

Date:

18-Oct-04 Release date: 26-Oct-04

Supersedes:

1ti9

Protein chain

P0ACH5  (MARA_ECOLI) -  Multiple antibiotic resistance protein marA

Seq: 127 a.a.

Struc: 129 a.a.

Protein chain

P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha

Seq: 329 a.a.

Struc: 81 a.a.

Enzyme reactions

• Enzyme class: Chain D: 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: intracellular (1 term)
• Biological process: response to antibiotic (4 terms)
• Biochemical function: DNA binding (4 terms)

reference

DOI no: 10.1111/j.1365-2958.2004.04250.x

Mol Microbiol 54:45-59 (2004)

PubMed id: 15458404

Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA.

B.Dangi, A.M.Gronenborn, J.L.Rosner, R.G.Martin.

ABSTRACT

The transcriptional activator, MarA, interacts with RNA polymerase (RNAP) to activate promoters of the mar regulon. Here, we identify the interacting surfaces of MarA and of the carboxy-terminal domain of the alpha subunit of RNAP (alpha-CTD) by NMR-based chemical shift mapping. Spectral changes were monitored for a MarA-DNA complex upon titration with alpha-CTD, and for alpha-CTD upon titration with MarA-DNA. The mapping results were confirmed by mutational studies and retention chromatography. A model of the ternary complex shows that alpha-CTD uses a '265-like determinant' to contact MarA at a surface distant from the DNA. This is unlike the interaction of alpha-CTD with the CRP or Fis activators where the '265 determinant' contacts DNA while another surface of the same alpha-CTD molecule contacts the activator. These results reveal a new versatility for alpha-CTD in transcriptional activation.