PDBsum entry 3dxj

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protein ligands metals Protein-protein interface(s) links
Transcription,transferase PDB id
Protein chains
231 a.a. *
243 a.a. *
1119 a.a. *
1504 a.a. *
95 a.a. *
349 a.a. *
PO4 ×2
MPD ×3
NE6 ×2
_MG ×3
_ZN ×4
Waters ×30
* Residue conservation analysis
PDB id:
Name: Transcription,transferase
Title: Crystal structure of thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic myxopyronin
Structure: DNA-directed RNA polymerase subunit alpha. Chain a, b, k, l. Chain: a, b, k, l. Bactrial RNA polymerase beta subunit. Chain c, m. Chain: c, m. Bactrial RNA polymerase beta-prime subunit. Chain d, n. Chain: d, n. Bactrial RNA polymerase omega subunit. Chain e,
Source: Thermus thermophilus hb8. Organism_taxid: 300852. Organism_taxid: 300852
3.00Å     R-factor:   0.235     R-free:   0.289
Authors: K.Das,E.Arnold
Key ref:
J.Mukhopadhyay et al. (2008). The RNA polymerase "switch region" is a target for inhibitors. Cell, 135, 295-307. PubMed id: 18957204 DOI: 10.1016/j.cell.2008.09.033
24-Jul-08     Release date:   14-Oct-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q5SHR6  (RPOA_THET8) -  DNA-directed RNA polymerase subunit alpha
315 a.a.
231 a.a.
Protein chains
Pfam   ArchSchema ?
Q5SHR6  (RPOA_THET8) -  DNA-directed RNA polymerase subunit alpha
315 a.a.
243 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE9  (RPOB_THET8) -  DNA-directed RNA polymerase subunit beta
1119 a.a.
1119 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE8  (RPOC_THET8) -  DNA-directed RNA polymerase subunit beta'
1524 a.a.
1504 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega
99 a.a.
95 a.a.*
Protein chains
Pfam   ArchSchema ?
Q5SKW1  (Q5SKW1_THET8) -  RNA polymerase sigma factor SigA
423 a.a.
349 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, K, L, M, N, O: E.C.  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
Bound ligand (Het Group name = PO4)
matches with 55.00% similarity
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     transcription initiation from bacterial-type RNA polymerase promoter   5 terms 
  Biochemical function     transferase activity     9 terms  


DOI no: 10.1016/j.cell.2008.09.033 Cell 135:295-307 (2008)
PubMed id: 18957204  
The RNA polymerase "switch region" is a target for inhibitors.
J.Mukhopadhyay, K.Das, S.Ismail, D.Koppstein, M.Jang, B.Hudson, S.Sarafianos, S.Tuske, J.Patel, R.Jansen, H.Irschik, E.Arnold, R.H.Ebright.
The alpha-pyrone antibiotic myxopyronin (Myx) inhibits bacterial RNA polymerase (RNAP). Here, through a combination of genetic, biochemical, and structural approaches, we show that Myx interacts with the RNAP "switch region"--the hinge that mediates opening and closing of the RNAP active center cleft--to prevent interaction of RNAP with promoter DNA. We define the contacts between Myx and RNAP and the effects of Myx on RNAP conformation and propose that Myx functions by interfering with opening of the RNAP active-center cleft during transcription initiation. We further show that the structurally related alpha-pyrone antibiotic corallopyronin (Cor) and the structurally unrelated macrocyclic-lactone antibiotic ripostatin (Rip) function analogously to Myx. The RNAP switch region is distant from targets of previously characterized RNAP inhibitors, and, correspondingly, Myx, Cor, and Rip do not exhibit crossresistance with previously characterized RNAP inhibitors. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.
  Selected figure(s)  
Figure 1.
Figure 1. RNAP Clamp, RNAP Switch Region, and Antibiotics Studied
(A) Conformational states of the RNAP clamp (two orthogonal views). Structure of RNAP showing open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Circle, switch region; dashed circle, binding site for rifamycins; violet sphere, active-center Mg^2+.
(B) Conformational states of the RNAP switch region (stereoview). Structure of RNAP switch 1 and RNAP switch 2 (β′ residues 1304–1329 and β′ residues 330–349; residues numbered as in E. coli RNAP) showing conformational states associated with open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Gray squares, points of connection of switch 1 and switch 2 to the RNAP main mass. Colored circles, points of connection of switch 1 and switch 2 to the RNAP clamp.
(C) Structures of myxopyronin A (Myx), corallopyronin A (Cor), and ripostatin A (Rip).
Figure 4.
Figure 4. Structural Basis of Transcription Inhibition by Myx: Structure of the RNAP-Myx Complex
(A) Overall structure (two orthogonal views; β′ nonconserved region and σ omitted for clarity). View orientations are as in Figure 1A. Green, Myx; violet sphere, active-center Mg^2+.
(B) Myx binding region (stereoview). Residues are numbered both as in T. thermophilus RNAP and as in E. coli RNAP (in parentheses). Green, Myx; red, sites of single-residue substitutions that confer high-level resistance to Myx.
  The above figures are reprinted from an Open Access publication published by Cell Press: Cell (2008, 135, 295-307) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22266819 K.Das, S.E.Martinez, J.D.Bauman, and E.Arnold (2012).
HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
  Nat Struct Mol Biol, 19, 253-259.
PDB codes: 3v4i 3v6d 3v81
21513713 A.Fabbretti, C.O.Gualerzi, and L.Brandi (2011).
How to cope with the quest for new antibiotics.
  FEBS Lett, 585, 1673-1681.  
  21477256 T.I.Moy, A.Daniel, C.Hardy, A.Jackson, O.Rehrauer, Y.S.Hwang, D.Zou, K.Nguyen, J.A.Silverman, Q.Li, and C.Murphy (2011).
Evaluating the activity of the RNA polymerase inhibitor myxopyronin B against Staphylococcus aureus.
  FEMS Microbiol Lett, 319, 176-179.  
20562828 A.Tupin, M.Gualtieri, J.P.Leonetti, and K.Brodolin (2010).
The transcription inhibitor lipiarmycin blocks DNA fitting into the RNA polymerase catalytic site.
  EMBO J, 29, 2527-2537.  
20457751 D.Pupov, N.Miropolskaya, A.Sevostyanova, I.Bass, I.Artsimovitch, and A.Kulbachinskiy (2010).
Multiple roles of the RNA polymerase {beta}' SW2 region in transcription initiation, promoter escape, and RNA elongation.
  Nucleic Acids Res, 38, 5784-5796.  
20432457 J.Wu, Q.Long, and J.Xie (2010).
(p)ppGpp and drug resistance.
  J Cell Physiol, 224, 300-304.  
20551974 K.J.Simmons, I.Chopra, and C.W.Fishwick (2010).
Structure-based discovery of antibacterial drugs.
  Nat Rev Microbiol, 8, 501-510.  
20520915 K.J.Weissman, and R.Müller (2010).
Myxobacterial secondary metabolites: bioactivities and modes-of-action.
  Nat Prod Rep, 27, 1276-1295.  
20503218 O.Erol, T.F.Schäberle, A.Schmitz, S.Rachid, C.Gurgui, M.El Omari, F.Lohr, S.Kehraus, J.Piel, R.Müller, and G.M.König (2010).
Biosynthesis of the myxobacterial antibiotic corallopyronin A.
  Chembiochem, 11, 1253-1265.  
20439713 P.C.Burrows, N.Joly, and M.Buck (2010).
A prehydrolysis state of an AAA+ ATPase supports transcription activation of an enhancer-dependent RNA polymerase.
  Proc Natl Acad Sci U S A, 107, 9376-9381.  
21124318 S.Tagami, S.Sekine, T.Kumarevel, N.Hino, Y.Murayama, S.Kamegamori, M.Yamamoto, K.Sakamoto, and S.Yokoyama (2010).
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
  Nature, 468, 978-982.
PDB codes: 3aoh 3aoi
19895816 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
  J Mol Biol, 395, 686-704.  
19324058 A.Ivetac, and J.A.McCammon (2009).
Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations.
  J Mol Biol, 388, 644-658.  
19578065 A.Rogozina, E.Zaychikov, M.Buckle, H.Heumann, and B.Sclavi (2009).
DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37 degrees C and results in the accumulation of an off-pathway intermediate.
  Nucleic Acids Res, 37, 5390-5404.  
19257840 A.Tupin, M.Gualtieri, K.Brodolin, and J.P.Leonetti (2009).
Myxopyronin: a punch in the jaws of bacterial RNA polymerase.
  Future Microbiol, 4, 145-149.  
  19903881 B.P.Hudson, J.Quispe, S.Lara-González, Y.Kim, H.M.Berman, E.Arnold, R.H.Ebright, and C.L.Lawson (2009).
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.
  Proc Natl Acad Sci U S A, 106, 19830-19835.
PDB code: 3iyd
19492989 D.Grohmann, A.Hirtreiter, and F.Werner (2009).
RNAP subunits F/E (RPB4/7) are stably associated with archaeal RNA polymerase: using fluorescence anisotropy to monitor RNAP assembly in vitro.
  Biochem J, 421, 339-343.  
19391118 J.Wu, and J.Xie (2009).
Magic spot: (p) ppGpp.
  J Cell Physiol, 220, 297-302.  
19844638 S.C.Wenzel, and R.Müller (2009).
The impact of genomics on the exploitation of the myxobacterial secondary metabolome.
  Nat Prod Rep, 26, 1385-1407.  
19171784 S.T.Rutherford, C.L.Villers, J.H.Lee, W.Ross, and R.L.Gourse (2009).
Allosteric control of Escherichia coli rRNA promoter complexes by DksA.
  Genes Dev, 23, 236-248.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.