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PDBsum entry 1smy

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1smy
Jmol
Contents
Protein chains
229 a.a. *
1119 a.a. *
1392 a.a. *
95 a.a. *
345 a.a. *
Ligands
G4P ×2
Metals
_MG ×362
_ZN ×4
Waters ×9031
* Residue conservation analysis
PDB id:
1smy
Name: Transferase
Title: Structural basis for transcription regulation by alarmone ppgpp
Structure: DNA-directed RNA polymerase alpha chain. Chain: a, b, k, l. Synonym: rnap alpha subunit, transcriptase alpha chain, RNA polymerase alpha subunit. DNA-directed RNA polymerase beta chain. Chain: c, m. Synonym: rnap beta subunit, transcriptase beta chain, RNA polymerase beta subunit. DNA-directed RNA polymerase beta' chain.
Source: Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
Biol. unit: Hexamer (from PQS)
Resolution:
2.70Å     R-factor:   0.186     R-free:   0.266
Authors: I.Artsimovitch,V.Patlan,S.Sekine,M.N.Vassylyeva,T.Hosaka, K.Ochi,S.Yokoyama,D.G.Vassylyev,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
I.Artsimovitch et al. (2004). Structural basis for transcription regulation by alarmone ppGpp. Cell, 117, 299-310. PubMed id: 15109491 DOI: 10.1016/S0092-8674(04)00401-5
Date:
10-Mar-04     Release date:   18-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9Z9H6  (RPOA_THETH) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
315 a.a.
229 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE9  (RPOB_THET8) -  DNA-directed RNA polymerase subunit beta
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1119 a.a.
1119 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE8  (RPOC_THET8) -  DNA-directed RNA polymerase subunit beta'
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1524 a.a.
1392 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega
Seq:
Struc:
99 a.a.
95 a.a.*
Protein chains
Pfam   ArchSchema ?
Q72L95  (Q72L95_THET2) -  RNA polymerase sigma factor SigA
Seq:
Struc:
423 a.a.
345 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.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
Bound ligand (Het Group name = G4P)
matches with 41.00% similarity
+ 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!
  Cellular component     cytoplasm   1 term 
  Biological process     transcription initiation from bacterial-type RNA polymerase promoter   6 terms 
  Biochemical function     transferase activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(04)00401-5 Cell 117:299-310 (2004)
PubMed id: 15109491  
 
 
Structural basis for transcription regulation by alarmone ppGpp.
I.Artsimovitch, V.Patlan, S.Sekine, M.N.Vassylyeva, T.Hosaka, K.Ochi, S.Yokoyama, D.G.Vassylyev.
 
  ABSTRACT  
 
Guanosine-tetraphosphate (ppGpp) is a major regulator of stringent control, an adaptive response of bacteria to amino acid starvation. The 2.7 A resolution structure of the Thermus thermophilus RNA polymerase (RNAP) holoenzyme in complex with ppGpp reveals that ppGpp binds to the same site near the active center in both independent RNAP molecules in the crystal but in strikingly distinct orientations. Binding is symmetrical with respect to the two diphosphates of ppGpp and is relaxed with respect to the orientation of the nucleotide base. Different modes of ppGpp binding are coupled with asymmetry of the active site configurations. The results suggest that base pairing of ppGpp with cytosines in the nontemplate DNA strand might be an essential component of transcription control by ppGpp. We present experimental evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine residues during both transcription initiation and elongation.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. ppGpp Binding Site(A) Overall stereo view of the ppGpp bound to the RNAP (the RNAP1 molecule was used). ppGpp is shown as pink sticks. The protein surface is colored according to the electrostatic potentials (positive, negative, and neutral are dark blue, red, and white, respectively).(B and C) Stereo view of the active center and ppGpp binding site in RNAP1 and RNAP2, respectively. ppGpp are shown in 5′ (pink) (B) and 3′ (blue) (C) orientations. Mg^2+ ions and their coordination bonds are shown as large magenta spheres and cyan dashed sticks, respectively. Water molecules coordinating Mg^2+ ions are shown as small red spheres. Hydrogen bonds are represented by dashed black lines.
Figure 5.
Figure 5. A Model of the Open ComplexT and NT strands are in magenta and cyan, respectively. (A) Overall stereo view. RNAP is represented by the surface of the electrostatic potentials, as in Figure 3A. ppGpp is blue. σND1 and σND2 are the two N-terminal σ subunit domains. Tyr β′1093 (yellow) stacks on the dwDNA T base at the entrance of the active site. (B) Enlarged stereo view of the open complex in the vicinity of the active and ppGpp binding sites. ppGpp (blue) in the 3′ orientation forms a putative base pair (red dashes) with the NT cytosine.
 
  The above figures are reprinted by permission from Cell Press: Cell (2004, 117, 299-310) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21461674 D.Ning, Y.Qian, X.Miao, and C.Wen (2011).
Role of the all1549 (ana-rsh) Gene, A relA/spoT Homolog, of the Cyanobacterium Anabaena sp. PCC7120.
  Curr Microbiol, 62, 1767-1773.  
21299642 M.F.Traxler, V.M.Zacharia, S.Marquardt, S.M.Summers, H.T.Nguyen, S.E.Stark, and T.Conway (2011).
Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli.
  Mol Microbiol, 79, 830-845.  
21152511 S.Carneiro, S.G.Villas-Bôas, E.C.Ferreira, and I.Rocha (2011).
Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations.
  Mol Biosyst, 7, 899-910.  
21278708 U.Kanjee, I.Gutsche, E.Alexopoulos, B.Zhao, M.El Bakkouri, G.Thibault, K.Liu, S.Ramachandran, J.Snider, E.F.Pai, and W.A.Houry (2011).
Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase.
  EMBO J, 30, 931-944.
PDB codes: 3n75 3q16
20700605 B.Nadratowska-Wesołowska, M.Słomińska-Wojewódzka, R.Łyzeń, A.Wegrzyn, A.Szalewska-Pałasz, and G.Wegrzyn (2010).
Transcription regulation of the Escherichia coli pcnB gene coding for poly(A) polymerase I: roles of ppGpp, DksA and sigma factors.
  Mol Genet Genomics, 284, 289-305.  
  20473037 D.Grohmann, and F.Werner (2010).
Hold on!: RNA polymerase interactions with the nascent RNA modulate transcription elongation and termination.
  RNA Biol, 7, 310-315.  
20030732 D.López, and R.Kolter (2010).
Extracellular signals that define distinct and coexisting cell fates in Bacillus subtilis.
  FEMS Microbiol Rev, 34, 134-149.  
20818390 D.Sun, G.Lee, J.H.Lee, H.Y.Kim, H.W.Rhee, S.Y.Park, K.J.Kim, Y.Kim, B.Y.Kim, J.I.Hong, C.Park, H.E.Choy, J.H.Kim, Y.H.Jeon, and J.Chung (2010).
A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses.
  Nat Struct Mol Biol, 17, 1188-1194.
PDB codes: 3nqw 3nr1
20488875 G.Wang, Y.Tanaka, and K.Ochi (2010).
The G243D mutation (afsB mutation) in the principal sigma factor sigmaHrdB alters intracellular ppGpp level and antibiotic production in Streptomyces coelicolor A3(2).
  Microbiology, 156, 2384-2392.  
20208344 H.Nanamiya, and F.Kawamura (2010).
Towards an elucidation of the roles of the ribosome during different growth phases in Bacillus subtilis.
  Biosci Biotechnol Biochem, 74, 451-461.  
20432457 J.Wu, Q.Long, and J.Xie (2010).
(p)ppGpp and drug resistance.
  J Cell Physiol, 224, 300-304.  
20008510 K.Potrykus, H.Murphy, X.Chen, J.A.Epstein, and M.Cashel (2010).
Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL.
  Nucleic Acids Res, 38, 1636-1651.  
20545843 L.Siculella, F.Damiano, R.di Summa, S.M.Tredici, R.Alduina, G.V.Gnoni, and P.Alifano (2010).
Guanosine 5'-diphosphate 3'-diphosphate (ppGpp) as a negative modulator of polynucleotide phosphorylase activity in a 'rare' actinomycete.
  Mol Microbiol, 77, 716-729.  
20298615 N.A.Valdez-Cruz, L.Caspeta, N.O.Pérez, O.T.Ramírez, and M.A.Trujillo-Roldán (2010).
Production of recombinant proteins in E. coli by the heat inducible expression system based on the phage lambda pL and/or pR promoters.
  Microb Cell Fact, 9, 18.  
19047343 A.Talà, G.Wang, M.Zemanova, S.Okamoto, K.Ochi, and P.Alifano (2009).
Activation of dormant bacterial genes by Nonomuraea sp. strain ATCC 39727 mutant-type RNA polymerase.
  J Bacteriol, 191, 805-814.  
19896365 D.G.Vassylyev (2009).
Elongation by RNA polymerase: a race through roadblocks.
  Curr Opin Struct Biol, 19, 691-700.  
19331655 E.Carata, C.Peano, S.M.Tredici, F.Ferrari, A.Talà, G.Corti, S.Bicciato, G.De Bellis, and P.Alifano (2009).
Phenotypes and gene expression profiles of Saccharopolyspora erythraea rifampicin-resistant (rif) mutants affected in erythromycin production.
  Microb Cell Fact, 8, 18.  
19489723 E.Nudler (2009).
RNA polymerase active center: the molecular engine of transcription.
  Annu Rev Biochem, 78, 335-361.  
18946472 G.A.Belogurov, M.N.Vassylyeva, A.Sevostyanova, J.R.Appleman, A.X.Xiang, R.Lira, S.E.Webber, S.Klyuyev, E.Nudler, I.Artsimovitch, and D.G.Vassylyev (2009).
Transcription inactivation through local refolding of the RNA polymerase structure.
  Nature, 457, 332-335.
PDB code: 3eql
18948199 I.Artsimovitch, and T.M.Henkin (2009).
In vitro approaches to analysis of transcription termination.
  Methods, 47, 37-43.  
19391118 J.Wu, and J.Xie (2009).
Magic spot: (p) ppGpp.
  J Cell Physiol, 220, 297-302.  
18767190 L.Caspeta, N.Flores, N.O.Pérez, F.Bolívar, and O.T.Ramírez (2009).
The effect of heating rate on Escherichia coli metabolism, physiological stress, transcriptional response, and production of temperature-induced recombinant protein: a scale-down study.
  Biotechnol Bioeng, 102, 468-482.  
19838295 L.Olvera, A.Mendoza-Vargas, N.Flores, M.Olvera, J.C.Sigala, G.Gosset, E.Morett, and F.Bolívar (2009).
Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation.
  PLoS One, 4, e7466.  
19424178 M.D.Blankschien, J.H.Lee, E.D.Grace, C.W.Lennon, J.A.Halliday, W.Ross, R.L.Gourse, and C.Herman (2009).
Super DksAs: substitutions in DksA enhancing its effects on transcription initiation.
  EMBO J, 28, 1720-1731.  
19148274 M.D.Blankschien, K.Potrykus, E.Grace, A.Choudhary, D.Vinella, M.Cashel, and C.Herman (2009).
TraR, a homolog of a RNAP secondary channel interactor, modulates transcription.
  PLoS Genet, 5, e1000345.  
19201753 M.Sajish, S.Kalayil, S.K.Verma, V.K.Nandicoori, and B.Prakash (2009).
The significance of EXDD and RXKD motif conservation in Rel proteins.
  J Biol Chem, 284, 9115-9123.  
19759216 R.Łyzen, M.Kochanowska, G.Wegrzyn, and A.Szalewska-Palasz (2009).
Transcription from bacteriophage lambda pR promoter is regulated independently and antagonistically by DksA and ppGpp.
  Nucleic Acids Res, 37, 6655-6664.  
19447912 Y.Natori, K.Tagami, K.Murakami, S.Yoshida, O.Tanigawa, Y.Moh, K.Masuda, T.Wada, S.Suzuki, H.Nanamiya, Y.Tozawa, and F.Kawamura (2009).
Transcription activity of individual rrn operons in Bacillus subtilis mutants deficient in (p)ppGpp synthetase genes, relA, yjbM, and ywaC.
  J Bacteriol, 191, 4555-4561.  
18284577 A.Aberg, V.Shingler, and C.Balsalobre (2008).
Regulation of the fimB promoter: a case of differential regulation by ppGpp and DksA in vivo.
  Mol Microbiol, 67, 1223-1241.  
18359660 A.Srivatsan, and J.D.Wang (2008).
Control of bacterial transcription, translation and replication by (p)ppGpp.
  Curr Opin Microbiol, 11, 100-105.  
18272182 C.E.Vrentas, T.Gaal, M.B.Berkmen, S.T.Rutherford, S.P.Haugen, D.G.Vassylyev, W.Ross, and R.L.Gourse (2008).
Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation.
  J Mol Biol, 377, 551-564.  
18310410 G.Wang, T.Hosaka, and K.Ochi (2008).
Dramatic activation of antibiotic production in Streptomyces coelicolor by cumulative drug resistance mutations.
  Appl Environ Microbiol, 74, 2834-2840.  
18456813 J.Yun, B.Jeon, Y.W.Barton, P.Plummer, Q.Zhang, and S.Ryu (2008).
Role of the DksA-like protein in the pathogenesis and diverse metabolic activity of Campylobacter jejuni.
  J Bacteriol, 190, 4512-4520.  
18535838 K.Mizusawa, S.Masuda, and H.Ohta (2008).
Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana.
  Planta, 228, 553-562.  
18454629 K.Potrykus, and M.Cashel (2008).
(p)ppGpp: still magical?
  Annu Rev Microbiol, 62, 35-51.  
18408024 M.F.Pomares, P.A.Vincent, R.N.Farías, and R.A.Salomón (2008).
Protective action of ppGpp in microcin J25-sensitive strains.
  J Bacteriol, 190, 4328-4334.  
18430135 M.F.Traxler, S.M.Summers, H.T.Nguyen, V.M.Zacharia, G.A.Hightower, J.T.Smith, and T.Conway (2008).
The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli.
  Mol Microbiol, 68, 1128-1148.  
18353782 S.Lee, M.H.Kim, B.S.Kang, J.S.Kim, G.H.Kim, Y.G.Kim, and K.J.Kim (2008).
Crystal structure of Escherichia coli MazG, the regulator of nutritional stress response.
  J Biol Chem, 283, 15232-15240.
PDB codes: 3cra 3crc
18178586 S.Masuda, K.Mizusawa, T.Narisawa, Y.Tozawa, H.Ohta, and K.Takamiya (2008).
The bacterial stringent response, conserved in chloroplasts, controls plant fertilization.
  Plant Cell Physiol, 49, 135-141.  
  19704441 S.Masuda, Y.Tozawa, and H.Ohta (2008).
Possible targets of "magic spots" in plant signalling.
  Plant Signal Behav, 3, 1021-1023.  
18287032 S.P.Haugen, W.Ross, M.Manrique, and R.L.Gourse (2008).
Fine structure of the promoter-sigma region 1.2 interaction.
  Proc Natl Acad Sci U S A, 105, 3292-3297.  
18521075 S.P.Haugen, W.Ross, and R.L.Gourse (2008).
Advances in bacterial promoter recognition and its control by factors that do not bind DNA.
  Nat Rev Microbiol, 6, 507-519.  
18039766 T.Durfee, A.M.Hansen, H.Zhi, F.R.Blattner, and D.J.Jin (2008).
Transcription profiling of the stringent response in Escherichia coli.
  J Bacteriol, 190, 1084-1096.  
18835987 Y.N.Zhou, W.G.Coleman, Z.Yang, Y.Yang, N.Hodgson, F.Chen, and D.J.Jin (2008).
Regulation of cell growth during serum starvation and bacterial survival in macrophages by the bifunctional enzyme SpoT in Helicobacter pylori.
  J Bacteriol, 190, 8025-8032.  
  17666783 A.Szalewska-Palasz, G.Wegrzyn, and A.Wegrzyn (2007).
Mechanisms of physiological regulation of RNA synthesis in bacteria: new discoveries breaking old schemes.
  J Appl Genet, 48, 281-294.  
17456470 A.Szalewska-Palasz, L.U.Johansson, L.M.Bernardo, E.Skärfstad, E.Stec, K.Brännström, and V.Shingler (2007).
Properties of RNA polymerase bypass mutants: implications for the role of ppGpp and its co-factor DksA in controlling transcription dependent on sigma54.
  J Biol Chem, 282, 18046-18056.  
17581591 D.G.Vassylyev, M.N.Vassylyeva, J.Zhang, M.Palangat, I.Artsimovitch, and R.Landick (2007).
Structural basis for substrate loading in bacterial RNA polymerase.
  Nature, 448, 163-168.
PDB codes: 2o5j 2ppb
17462013 F.Cava, O.Laptenko, S.Borukhov, Z.Chahlafi, E.Blas-Galindo, P.Gómez-Puertas, and J.Berenguer (2007).
Control of the respiratory metabolism of Thermus thermophilus by the nitrate respiration conjugative element NCE.
  Mol Microbiol, 64, 630-646.  
17760833 H.J.Rhee, E.J.Kim, and J.K.Lee (2007).
Physiological polyamines: simple primordial stress molecules.
  J Cell Mol Med, 11, 685-703.  
17587668 K.Ochi (2007).
From microbial differentiation to ribosome engineering.
  Biosci Biotechnol Biochem, 71, 1373-1386.  
17334376 L.Bettendorff, B.Wirtzfeld, A.F.Makarchikov, G.Mazzucchelli, M.Frédérich, T.Gigliobianco, M.Gangolf, E.De Pauw, L.Angenot, and P.Wins (2007).
Discovery of a natural thiamine adenine nucleotide.
  Nat Chem Biol, 3, 211-212.  
17496080 L.U.Magnusson, B.Gummesson, P.Joksimović, A.Farewell, and T.Nyström (2007).
Identical, independent, and opposing roles of ppGpp and DksA in Escherichia coli.
  J Bacteriol, 189, 5193-5202.  
17804668 M.Kaczanowska, and M.Rydén-Aulin (2007).
Ribosome biogenesis and the translation process in Escherichia coli.
  Microbiol Mol Biol Rev, 71, 477-494.  
17911108 M.Sajish, D.Tiwari, D.Rananaware, V.K.Nandicoori, and B.Prakash (2007).
A charge reversal differentiates (p)ppGpp synthesis by monofunctional and bifunctional Rel proteins.
  J Biol Chem, 282, 34977-34983.  
17207814 S.T.Rutherford, J.J.Lemke, C.E.Vrentas, T.Gaal, W.Ross, and R.L.Gourse (2007).
Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase.
  J Mol Biol, 366, 1243-1257.  
17938177 Y.Tozawa, A.Nozawa, T.Kanno, T.Narisawa, S.Masuda, K.Kasai, and H.Nanamiya (2007).
Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants.
  J Biol Chem, 282, 35536-35545.  
  16511259 A.A.Perederina, M.N.Vassylyeva, I.A.Berezin, V.Svetlov, I.Artsimovitch, and D.G.Vassylyev (2006).
Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors GreB from Escherichia coli and Gfh1 from Thermus thermophilus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 44-46.  
16798040 A.Feklistov, N.Barinova, A.Sevostyanova, E.Heyduk, I.Bass, I.Vvedenskaya, K.Kuznedelov, E.Merkiene, E.Stavrovskaya, S.Klimasauskas, V.Nikiforov, T.Heyduk, K.Severinov, and A.Kulbachinskiy (2006).
A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme.
  Mol Cell, 23, 97.  
16690607 A.Kulbachinskiy, and A.Mustaev (2006).
Region 3.2 of the sigma subunit contributes to the binding of the 3'-initiating nucleotide in the RNA polymerase active center and facilitates promoter clearance during initiation.
  J Biol Chem, 281, 18273-18276.  
16847086 D.F.Warner, and V.Mizrahi (2006).
Tuberculosis chemotherapy: the influence of bacillary stress and damage response pathways on drug efficacy.
  Clin Microbiol Rev, 19, 558-570.  
17129781 D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, and R.D.Kornberg (2006).
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.
  Cell, 127, 941-954.
PDB codes: 2e2h 2e2i 2e2j 2nvq 2nvs 2nvt 2nvx 2nvy 2nvz 2yu9
16914440 E.Kashkina, M.Anikin, T.H.Tahirov, S.N.Kochetkov, D.G.Vassylyev, and D.Temiakov (2006).
Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations.
  Nucleic Acids Res, 34, 4036-4045.  
16298991 J.Symersky, A.Perederina, M.N.Vassylyeva, V.Svetlov, I.Artsimovitch, and D.G.Vassylyev (2006).
Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors.
  J Biol Chem, 281, 1309-1312.
PDB code: 2eul
16343907 K.Braeken, M.Moris, R.Daniels, J.Vanderleyden, and J.Michiels (2006).
New horizons for (p)ppGpp in bacterial and plant physiology.
  Trends Microbiol, 14, 45-54.  
17015650 K.Kasai, T.Nishizawa, K.Takahashi, T.Hosaka, H.Aoki, and K.Ochi (2006).
Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus.
  J Bacteriol, 188, 7111-7122.  
16855239 K.Mouery, B.A.Rader, E.C.Gaynor, and K.Guillemin (2006).
The stringent response is required for Helicobacter pylori survival of stationary phase, exposure to acid, and aerobic shock.
  J Bacteriol, 188, 5494-5500.  
16597620 K.Potrykus, D.Vinella, H.Murphy, A.Szalewska-Palasz, R.D'Ari, and M.Cashel (2006).
Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA.
  J Biol Chem, 281, 15238-15248.  
16629675 L.M.Bernardo, L.U.Johansson, D.Solera, E.Skärfstad, and V.Shingler (2006).
The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of sigma-dependent transcription.
  Mol Microbiol, 60, 749-764.  
16788203 N.Saito, J.Xu, T.Hosaka, S.Okamoto, H.Aoki, M.J.Bibb, and K.Ochi (2006).
EshA accentuates ppGpp accumulation and is conditionally required for antibiotic production in Streptomyces coelicolor A3(2).
  J Bacteriol, 188, 4952-4961.  
16788165 R.L.Gourse, W.Ross, and S.T.Rutherford (2006).
General pathway for turning on promoters transcribed by RNA polymerases containing alternative sigma factors.
  J Bacteriol, 188, 4589-4591.  
16777598 S.P.Haugen, M.B.Berkmen, W.Ross, T.Gaal, C.Ward, and R.L.Gourse (2006).
rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase.
  Cell, 125, 1069-1082.  
16524917 V.Trinh, M.F.Langelier, J.Archambault, and B.Coulombe (2006).
Structural perspective on mutations affecting the function of multisubunit RNA polymerases.
  Microbiol Mol Biol Rev, 70, 12-36.  
15687384 A.J.Smith, and N.J.Savery (2005).
RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair.
  Nucleic Acids Res, 33, 755-764.  
15780938 A.Maitra, I.Shulgina, and V.J.Hernandez (2005).
Conversion of active promoter-RNA polymerase complexes into inactive promoter bound complexes in E. coli by the transcription effector, ppGpp.
  Mol Cell, 17, 817-829.  
15899978 B.J.Paul, M.B.Berkmen, and R.L.Gourse (2005).
DksA potentiates direct activation of amino acid promoters by ppGpp.
  Proc Natl Acad Sci U S A, 102, 7823-7828.  
16204187 C.E.Vrentas, T.Gaal, W.Ross, R.H.Ebright, and R.L.Gourse (2005).
Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA.
  Genes Dev, 19, 2378-2387.  
16273103 D.G.Vassylyev, V.Svetlov, M.N.Vassylyeva, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, and I.Artsimovitch (2005).
Structural basis for transcription inhibition by tagetitoxin.
  Nat Struct Mol Biol, 12, 1086-1093.
PDB code: 2be5
16167380 D.Temiakov, N.Zenkin, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, E.Kashkina, M.Savkina, S.Zorov, V.Nikiforov, N.Igarashi, N.Matsugaki, S.Wakatsuki, K.Severinov, and D.G.Vassylyev (2005).
Structural basis of transcription inhibition by antibiotic streptolydigin.
  Mol Cell, 19, 655-666.
PDB code: 2a6h
15853883 D.Vinella, C.Albrecht, M.Cashel, and R.D'Ari (2005).
Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli.
  Mol Microbiol, 56, 958-970.  
16096056 I.Artsimovitch, M.N.Vassylyeva, D.Svetlov, V.Svetlov, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, T.H.Tahirov, and D.G.Vassylyev (2005).
Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.
  Cell, 122, 351-363.
PDB codes: 2a68 2a69 2a6e
15686546 J.D.Gralla (2005).
Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein.
  Mol Microbiol, 55, 973-977.  
15866041 L.U.Magnusson, A.Farewell, and T.Nyström (2005).
ppGpp: a global regulator in Escherichia coli.
  Trends Microbiol, 13, 236-242.  
16122422 S.Tuske, S.G.Sarafianos, X.Wang, B.Hudson, E.Sineva, J.Mukhopadhyay, J.J.Birktoft, O.Leroy, S.Ismail, A.D.Clark, C.Dharia, A.Napoli, O.Laptenko, J.Lee, S.Borukhov, R.H.Ebright, and E.Arnold (2005).
Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.
  Cell, 122, 541-552.
PDB codes: 1zyr 2cw0
15294156 A.Perederina, V.Svetlov, M.N.Vassylyeva, T.H.Tahirov, S.Yokoyama, I.Artsimovitch, and D.G.Vassylyev (2004).
Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription.
  Cell, 118, 297-309.
PDB code: 1tjl
15294154 B.E.Nickels, and A.Hochschild (2004).
Regulation of RNA polymerase through the secondary channel.
  Cell, 118, 281-284.  
15294157 B.J.Paul, M.M.Barker, W.Ross, D.A.Schneider, C.Webb, J.W.Foster, and R.L.Gourse (2004).
DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP.
  Cell, 118, 311-322.  
15568992 B.J.Paul, W.Ross, T.Gaal, and R.L.Gourse (2004).
rRNA transcription in Escherichia coli.
  Annu Rev Genet, 38, 749-770.  
15537538 K.D.Westover, D.A.Bushnell, and R.D.Kornberg (2004).
Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
  Cell, 119, 481-489.
PDB codes: 1r9s 1r9t 1twa 1twc 1twf 1twg 1twh
15507686 K.Kasai, T.Kanno, Y.Endo, K.Wakasa, and Y.Tozawa (2004).
Guanosine tetra- and pentaphosphate synthase activity in chloroplasts of a higher plant: association with 70S ribosomes and inhibition by tetracycline.
  Nucleic Acids Res, 32, 5732-5741.  
15496987 L.Krásný, and R.L.Gourse (2004).
An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation.
  EMBO J, 23, 4473-4483.  
15590778 P.P.Dennis, M.Ehrenberg, and H.Bremer (2004).
Control of rRNA synthesis in Escherichia coli: a systems biology approach.
  Microbiol Mol Biol Rev, 68, 639-668.  
15262972 V.Svetlov, D.G.Vassylyev, and I.Artsimovitch (2004).
Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase.
  J Biol Chem, 279, 38087-38090.  
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.