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PDBsum entry 1tjl

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protein metals Protein-protein interface(s) links
Transcription PDB id
1tjl
Jmol
Contents
Protein chains
(+ 4 more) 145 a.a. *
Metals
_ZN ×10
Waters ×1022
* Residue conservation analysis
PDB id:
1tjl
Name: Transcription
Title: Crystal structure of transcription factor dksa from e. Coli
Structure: Dnak suppressor protein. Chain: a, b, c, d, e, f, g, h, i, j. Synonym: dksa, transcription factor. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: dksa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.228     R-free:   0.268
Authors: A.Perederina,V.Svetlov,M.N.Vassylyeva,I.Artsimovitch,S.Yokoy D.G.Vassylyev,Riken Structural Genomics/proteomics Initiati
Key ref:
A.Perederina et al. (2004). Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell, 118, 297-309. PubMed id: 15294156 DOI: 10.1016/j.cell.2004.06.030
Date:
06-Jun-04     Release date:   07-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0ABS1  (DKSA_ECOLI) -  RNA polymerase-binding transcription factor DksA
Seq:
Struc:
151 a.a.
145 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     regulation of gene expression   1 term 
  Biochemical function     metal ion binding     2 terms  

 

 
DOI no: 10.1016/j.cell.2004.06.030 Cell 118:297-309 (2004)
PubMed id: 15294156  
 
 
Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription.
A.Perederina, V.Svetlov, M.N.Vassylyeva, T.H.Tahirov, S.Yokoyama, I.Artsimovitch, D.G.Vassylyev.
 
  ABSTRACT  
 
Bacterial transcription is regulated by the alarmone ppGpp, which binds near the catalytic site of RNA polymerase (RNAP) and modulates its activity. We show that the DksA protein is a crucial component of ppGpp-dependent regulation. The 2.0 A resolution structure of Escherichia coli DksA reveals a globular domain and a coiled coil with two highly conserved Asp residues at its tip that is reminiscent of the transcript cleavage factor GreA. This structural similarity suggests that DksA coiled coil protrudes into the RNAP secondary channel to coordinate a ppGpp bound Mg2+ ion with the Asp residues, thereby stabilizing the ppGpp-RNAP complex. Biochemical analysis demonstrates that DksA affects transcript elongation, albeit differently from GreA; augments ppGpp effects on initiation; and binds directly to RNAP, positioning the Asp residues near the active site. Substitution of these residues eliminates the synergy between DksA and ppGpp. Thus, the secondary channel emerges as a common regulatory entrance for transcription factors.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Amino Acid Sequence Alignment of Several DksA HomologsConsensus sequence is shown above the alignment; the numbering corresponds to that of the E. coli DksA. The height of the colored bars on top indicates sequence conservation. Red, 100%; dark blue, <50%; others indicate intermediate levels of identity. C4-type Zn finger motif is shown as a gray bar. As predicted by COILS (Lupas, 1996), regions 33–54 and 74–110 exhibit strong propensity toward formation of the coiled-coil structures (shown as ribbons). Residues identical to those in E. coli DksA are white on black squares.
Figure 2.
Figure 2. Structure of DksA and Structural Similarity with GreA(A and B) Ribbon diagrams of DksA (A) and GreA (B) structures. The CC, globular domains and α turns between the α helices of the CC in the proteins are shown in cyan, yellow, and green, respectively. The invariant acidic residues at the tips of the CCs are shown as red ball-and-stick models. (A) In DksA, Zn^2+ ion (red sphere) is coordinated by four cysteine residues (green ball-and-stick models); the CT helix is in orange.(C) DksA (blue) and GreA (yellow) are superimposed by their CC domains. The conserved acidic residues in the α turns of the proteins are shown as blue (DksA) and yellow (GreA) ball-and-stick models.(D and E) Sequence alignments of GreA (D) and DksA (E) proteins in the vicinity of the invariant acidic residues, which are highlighted by pink boxes.(F) Superposition of the DksA (blue) and GreA (yellow) α turns.
 
  The above figures are reprinted by permission from Cell Press: Cell (2004, 118, 297-309) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22669220 H.Merrikh, Y.Zhang, A.D.Grossman, and J.D.Wang (2012).
Replication-transcription conflicts in bacteria.
  Nat Rev Microbiol, 10, 449-458.  
21453489 A.R.Poteete (2011).
Recombination phenotypes of Escherichia coli greA mutants.
  BMC Mol Biol, 12, 12.  
21255113 C.E.Blaby-Haas, R.Furman, D.A.Rodionov, I.Artsimovitch, and V.de Crécy-Lagard (2011).
Role of a Zn-independent DksA in Zn homeostasis and stringent response.
  Mol Microbiol, 79, 700-715.  
21402902 J.J.Lemke, P.Sanchez-Vazquez, H.L.Burgos, G.Hedberg, W.Ross, and R.L.Gourse (2011).
Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA.
  Proc Natl Acad Sci U S A, 108, 5712-5717.  
20946586 K.Potrykus, H.Murphy, N.Philippe, and M.Cashel (2011).
ppGpp is the major source of growth rate control in E. coli.
  Environ Microbiol, 13, 563-575.  
20478253 A.K.Tehranchi, M.D.Blankschien, Y.Zhang, J.A.Halliday, A.Srivatsan, J.Peng, C.Herman, and J.D.Wang (2010).
The transcription factor DksA prevents conflicts between DNA replication and transcription machinery.
  Cell, 141, 595-605.  
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.  
20371514 D.García-Moreno, J.Abellón-Ruiz, F.García-Heras, F.J.Murillo, S.Padmanabhan, and M.Elías-Arnanz (2010).
CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD.
  Nucleic Acids Res, 38, 4586-4598.  
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.  
20702425 L.F.Westblade, E.A.Campbell, C.Pukhrambam, J.C.Padovan, B.E.Nickels, V.Lamour, and S.A.Darst (2010).
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.
  Nucleic Acids Res, 38, 8357-8369.
PDB code: 3mlq
20221735 M.Song, H.J.Kim, S.Ryu, H.Yoon, J.Yun, and H.E.Choy (2010).
ppGpp-mediated stationary phase induction of the genes encoded by horizontally acquired pathogenicity islands and cob/pdu locus in Salmonella enterica serovar Typhimurium.
  J Microbiol, 48, 89-95.  
19895816 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
  J Mol Biol, 395, 686-704.  
20534498 Y.Yuzenkova, and N.Zenkin (2010).
Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis.
  Proc Natl Acad Sci U S A, 107, 10878-10883.  
20199605 Z.D.Dalebroux, B.F.Yagi, T.Sahr, C.Buchrieser, and M.S.Swanson (2010).
Distinct roles of ppGpp and DksA in Legionella pneumophila differentiation.
  Mol Microbiol, 76, 200-219.  
19251846 A.Aberg, J.Fernández-Vázquez, J.D.Cabrer-Panes, A.Sánchez, and C.Balsalobre (2009).
Similar and divergent effects of ppGpp and DksA deficiencies on transcription in Escherichia coli.
  J Bacteriol, 191, 3226-3236.  
19596241 C.L.Stallings, N.C.Stephanou, L.Chu, A.Hochschild, B.E.Nickels, and M.S.Glickman (2009).
CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence.
  Cell, 138, 146-159.  
19617357 C.W.Lennon, T.Gaal, W.Ross, and R.L.Gourse (2009).
Escherichia coli DksA binds to Free RNA polymerase with higher affinity than to RNA polymerase in an open complex.
  J Bacteriol, 191, 5854-5858.  
19896365 D.G.Vassylyev (2009).
Elongation by RNA polymerase: a race through roadblocks.
  Curr Opin Struct Biol, 19, 691-700.  
19251845 D.García-Moreno, M.C.Polanco, G.Navarro-Avilés, F.J.Murillo, S.Padmanabhan, and M.Elías-Arnanz (2009).
A vitamin B12-based system for conditional expression reveals dksA to be an essential gene in Myxococcus xanthus.
  J Bacteriol, 191, 3108-3119.  
19489723 E.Nudler (2009).
RNA polymerase active center: the molecular engine of transcription.
  Annu Rev Biochem, 78, 335-361.  
19876386 J.C.Charity, L.T.Blalock, M.M.Costante-Hamm, D.L.Kasper, and S.L.Dove (2009).
Small molecule control of virulence gene expression in Francisella tularensis.
  PLoS Pathog, 5, e1000641.  
19391118 J.Wu, and J.Xie (2009).
Magic spot: (p) ppGpp.
  J Cell Physiol, 220, 297-302.  
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.  
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.  
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.  
18086212 A.Costanzo, H.Nicoloff, S.E.Barchinger, A.B.Banta, R.L.Gourse, and S.E.Ades (2008).
ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms.
  Mol Microbiol, 67, 619-632.  
17680684 A.Kuroda, T.Nishimura, T.Ishida, R.Hirota, and K.Nomura (2008).
Detection of chrysotile asbestos by using a chrysotile-binding protein.
  Biotechnol Bioeng, 99, 285-289.  
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.  
18452582 C.L.Turnbough (2008).
Regulation of bacterial gene expression by the NTP substrates of transcription initiation.
  Mol Microbiol, 69, 10-14.  
18729732 J.W.Roberts, S.Shankar, and J.J.Filter (2008).
RNA polymerase elongation factors.
  Annu Rev Microbiol, 62, 211-233.  
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.  
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.  
18532980 R.Harinarayanan, H.Murphy, and M.Cashel (2008).
Synthetic growth phenotypes of Escherichia coli lacking ppGpp and transketolase A (tktA) are due to ppGpp-mediated transcriptional regulation of tktB.
  Mol Microbiol, 69, 882-894.  
18280161 S.Borukhov, and E.Nudler (2008).
RNA polymerase: the vehicle of transcription.
  Trends Microbiol, 16, 126-134.  
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.  
18760284 V.Lamour, S.T.Rutherford, K.Kuznedelov, U.A.Ramagopal, R.L.Gourse, K.Severinov, and S.A.Darst (2008).
Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein.
  J Mol Biol, 383, 367-379.
PDB code: 3bmb
17021938 A.Collet, S.Vilain, P.Cosette, G.A.Junter, T.Jouenne, R.S.Phillips, and P.Di Martino (2007).
Protein expression in Escherichia coli S17-1 biofilms: impact of indole.
  Antonie Van Leeuwenhoek, 91, 71-85.  
17951384 A.Hochschild (2007).
Gene-specific regulation by a transcript cleavage factor: facilitating promoter escape.
  J Bacteriol, 189, 8769-8771.  
  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.  
17332743 A.Typas, C.Barembruch, A.Possling, and R.Hengge (2007).
Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of sigmas activity and levels.
  EMBO J, 26, 1569-1578.  
17302812 A.Typas, G.Becker, and R.Hengge (2007).
The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase.
  Mol Microbiol, 63, 1296-1306.  
17532339 D.G.Vassylyev, and J.Symersky (2007).
Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications.
  J Mol Biol, 370, 417-426.
PDB code: 2pnq
17766423 E.Stepanova, J.Lee, M.Ozerova, E.Semenova, K.Datsenko, B.L.Wanner, K.Severinov, and S.Borukhov (2007).
Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro.
  J Bacteriol, 189, 8772-8785.  
17434131 G.A.Belogurov, M.N.Vassylyeva, V.Svetlov, S.Klyuyev, N.V.Grishin, D.G.Vassylyev, and I.Artsimovitch (2007).
Structural basis for converting a general transcription factor into an operon-specific virulence regulator.
  Mol Cell, 26, 117-129.
PDB code: 2oug
17913712 J.Ye, S.H.Cho, J.Fuselier, W.Li, J.Beckwith, and T.A.Rapoport (2007).
Crystal structure of an unusual thioredoxin protein with a zinc finger domain.
  J Biol Chem, 282, 34945-34951.  
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.  
17216653 P.F.Suthers, R.L.Gourse, and J.Yin (2007).
Rapid responses of ribosomal RNA synthesis to nutrient shifts.
  Biotechnol Bioeng, 97, 1230-1245.  
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.  
16882986 A.A.Mahdi, C.Buckman, L.Harris, and R.G.Lloyd (2006).
Rep and PriA helicase activities prevent RecA from provoking unnecessary recombination during replication fork repair.
  Genes Dev, 20, 2135-2147.  
  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.  
16788171 A.Costanzo, and S.E.Ades (2006).
Growth phase-dependent regulation of the extracytoplasmic stress factor, sigmaE, by guanosine 3',5'-bispyrophosphate (ppGpp).
  J Bacteriol, 188, 4627-4634.  
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
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.  
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.  
16629670 K.V.Newell, D.P.Thomas, D.Brekasis, and M.S.Paget (2006).
The RNA polymerase-binding protein RbpA confers basal levels of rifampicin resistance on Streptomyces coelicolor.
  Mol Microbiol, 60, 687-696.  
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.  
16879646 M.Peñalver-Mellado, F.García-Heras, S.Padmanabhan, D.García-Moreno, F.J.Murillo, and M.Elías-Arnanz (2006).
Recruitment of a novel zinc-bound transcriptional factor by a bacterial HMGA-type protein is required for regulating multiple processes in Myxococcus xanthus.
  Mol Microbiol, 61, 910-926.  
16553885 M.Susa, T.Kubori, and N.Shimamoto (2006).
A pathway branching in transcription initiation in Escherichia coli.
  Mol Microbiol, 59, 1807-1817.  
16628221 O.Laptenko, S.S.Kim, J.Lee, M.Starodubtseva, F.Cava, J.Berenguer, X.P.Kong, and S.Borukhov (2006).
pH-dependent conformational switch activates the inhibitor of transcription elongation.
  EMBO J, 25, 2131-2141.
PDB code: 2f23
16815708 P.Deighan, and A.Hochschild (2006).
Conformational toggle triggers a modulator of RNA polymerase activity.
  Trends Biochem Sci, 31, 424-426.  
16885445 P.Mallik, B.J.Paul, S.T.Rutherford, R.L.Gourse, and R.Osuna (2006).
DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli.
  J Bacteriol, 188, 5775-5782.  
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.  
16472307 V.Venturi (2006).
Regulation of quorum sensing in Pseudomonas.
  FEMS Microbiol Rev, 30, 274-291.  
16475805 W.S.Kontur, R.M.Saecker, C.A.Davis, M.W.Capp, and M.T.Record (2006).
Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subsequent conversion to RPo.
  Biochemistry, 45, 2161-2177.  
15685225 A.Travers, and G.Muskhelishvili (2005).
DNA supercoiling - a global transcriptional regulator for enterobacterial growth?
  Nat Rev Microbiol, 3, 157-169.  
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.  
16039593 B.W.Trautinger, R.P.Jaktaji, E.Rusakova, and R.G.Lloyd (2005).
RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription.
  Mol Cell, 19, 247-258.  
16135230 C.D.Hardy, and N.R.Cozzarelli (2005).
A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure.
  Mol Microbiol, 57, 1636-1652.  
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
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.  
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.  
15774887 J.L.Dahl, K.Arora, H.I.Boshoff, D.C.Whiteford, S.A.Pacheco, O.J.Walsh, D.Lau-Bonilla, W.B.Davis, and A.G.Garza (2005).
The relA homolog of Mycobacterium smegmatis affects cell appearance, viability, and gene expression.
  J Bacteriol, 187, 2439-2447.  
15864262 K.Gerdes, S.K.Christensen, and A.Løbner-Olesen (2005).
Prokaryotic toxin-antitoxin stress response loci.
  Nat Rev Microbiol, 3, 371-382.  
15853892 K.Perron, R.Comte, and C.van Delden (2005).
DksA represses ribosomal gene transcription in Pseudomonas aeruginosa by interacting with RNA polymerase on ribosomal promoters.
  Mol Microbiol, 56, 1087-1102.  
15866041 L.U.Magnusson, A.Farewell, and T.Nyström (2005).
ppGpp: a global regulator in Escherichia coli.
  Trends Microbiol, 13, 236-242.  
15720542 S.Borukhov, J.Lee, and O.Laptenko (2005).
Bacterial transcription elongation factors: new insights into molecular mechanism of action.
  Mol Microbiol, 55, 1315-1324.  
16135220 S.Deng, R.A.Stein, and N.P.Higgins (2005).
Organization of supercoil domains and their reorganization by transcription.
  Mol Microbiol, 57, 1511-1521.  
15948952 T.R.Meddows, A.P.Savory, J.I.Grove, T.Moore, and R.G.Lloyd (2005).
RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks.
  Mol Microbiol, 57, 97.  
15606780 A.Kulbachinskiy, A.Feklistov, I.Krasheninnikov, A.Goldfarb, and V.Nikiforov (2004).
Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB.
  Eur J Biochem, 271, 4921-4931.  
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.  
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.  
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 code is shown on the right.

 

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