PDBsum entry 1xs9

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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
Protein chains
129 a.a. *
81 a.a. *
* Residue conservation analysis
PDB id:
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
18-Oct-04     Release date:   26-Oct-04    
Supersedes: 1ti9
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0ACH5  (MARA_ECOLI) -  Multiple antibiotic resistance protein MarA
127 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha
329 a.a.
81 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain D: E.C.  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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 
  GO annot!
  Biological process     response to antibiotic   5 terms 
  Biochemical function     DNA binding     4 terms  


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.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20453091 L.M.McMurry, and S.B.Levy (2010).
Evidence that regulatory protein MarA of Escherichia coli represses rob by steric hindrance.
  J Bacteriol, 192, 3977-3982.  
19251886 D.Klein-Marcuschamer, C.N.Santos, H.Yu, and G.Stephanopoulos (2009).
Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes.
  Appl Environ Microbiol, 75, 2705-2711.  
19289129 K.L.Griffith, M.M.Fitzpatrick, E.F.Keen, and R.E.Wolf (2009).
Two functions of the C-terminal domain of Escherichia coli Rob: mediating "sequestration-dispersal" as a novel off-on switch for regulating Rob's activity as a transcription activator and preventing degradation of Rob by Lon protease.
  J Mol Biol, 388, 415-430.  
20019803 M.E.Wall, D.A.Markowitz, J.L.Rosner, and R.G.Martin (2009).
Model of transcriptional activation by MarA in Escherichia coli.
  PLoS Comput Biol, 5, e1000614.  
18366439 A.Kolin, V.Balasubramaniam, J.M.Skredenske, J.R.Wickstrum, and S.M.Egan (2008).
Differences in the mechanism of the allosteric l-rhamnose responses of the AraC/XylS family transcription activators RhaS and RhaR.
  Mol Microbiol, 68, 448-461.  
18466918 I.Lozada-Chávez, V.E.Angarica, J.Collado-Vides, and B.Contreras-Moreira (2008).
The role of DNA-binding specificity in the evolution of bacterial regulatory networks.
  J Mol Biol, 379, 627-643.  
18849430 M.Bellair, and J.H.Withey (2008).
Flexibility of Vibrio cholerae ToxT in transcription activation of genes having altered promoter spacing.
  J Bacteriol, 190, 7925-7931.  
17997097 L.L.Beck, T.G.Smith, and T.R.Hoover (2007).
Look, no hands! Unconventional transcriptional activators in bacteria.
  Trends Microbiol, 15, 530-537.  
16478729 T.Schneiders, and S.B.Levy (2006).
MarA-mediated transcriptional repression of the rob promoter.
  J Biol Chem, 281, 10049-10055.  
16122968 A.M.Bonvin, R.Boelens, and R.Kaptein (2005).
NMR analysis of protein interactions.
  Curr Opin Chem Biol, 9, 501-508.  
15853893 K.L.Griffith, S.M.Becker, and R.E.Wolf (2005).
Characterization of TetD as a transcriptional activator of a subset of genes of the Escherichia coli SoxS/MarA/Rob regulon.
  Mol Microbiol, 56, 1103-1117.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.