PDBsum entry 2eul

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protein metals Protein-protein interface(s) links
Transcription PDB id
Protein chains
156 a.a. *
_ZN ×25
Waters ×386
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Structure of the transcription factor gfh1.
Structure: Anti-cleavage anti-grea transcription factor gfh1 chain: a, b, c, d. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: gfhi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Not given
2.40Å     R-factor:   0.206     R-free:   0.245
Authors: J.Symersky,A.Perederina,M.N.Vassylyeva,V.Svetlov,I.Artsimovi D.G.Vassylyev,Riken Structural Genomics/proteomics Initiati
Key ref:
J.Symersky et al. (2006). Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors. J Biol Chem, 281, 1309-1312. PubMed id: 16298991 DOI: 10.1074/jbc.C500405200
28-Oct-05     Release date:   15-Nov-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q5SJG6  (Q5SJG6_THET8) -  Transcription inhibitor protein Gfh1
156 a.a.
156 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   3 terms 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1074/jbc.C500405200 J Biol Chem 281:1309-1312 (2006)
PubMed id: 16298991  
Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors.
J.Symersky, A.Perederina, M.N.Vassylyeva, V.Svetlov, I.Artsimovitch, D.G.Vassylyev.
Gre factors enhance the intrinsic endonucleolytic activity of RNA polymerase to rescue arrested transcription complexes and are thought to confer the high fidelity and processivity of RNA synthesis. The Gre factors insert the extended alpha-helical coiled-coil domains into the RNA polymerase secondary channel to position two invariant acidic residues at the coiled-coil tip near the active site to stabilize the catalytic metal ion. Gfh1, a GreA homolog from Thermus thermophilus, inhibits rather than activates RNA cleavage. Here we report the structure of the T. thermophilus Gfh1 at 2.4 A resolution revealing a two-domain architecture closely resembling that of GreA. However, the interdomain orientation is strikingly distinct (approximately 162 degrees rotation) between the two proteins. In contrast to GreA, which has two acidic residues on a well fixed self-stabilized alpha-turn, the tip of the Gfh1 coiled-coil is flexible and contains four acidic residues. This difference is likely the key to the Gre functional diversity, while Gfh1 inhibits exo- and endonucleolytic cleavage, RNA synthesis, and pyrophosphorolysis, GreA enhances only the endonucleolytic cleavage. We propose that Gfh1 acidic residues stabilize the RNA polymerase active center in a catalytically inactive configuration through Mg2+-mediated interactions. The excess of the acidic residues and inherent flexibility of the coiled-coil tip might allow Gfh1 to adjust its activity to structurally distinct substrates, thereby inhibiting diverse catalytic reactions of RNA polymerase.
  Selected figure(s)  
Figure 1.
The Gfh1 structure and comparison with GreA and DksA. A, alignment of the Gfh1 and GreA sequences. The residues with conserved chemical properties among Gfh1 and GreA sequences that might thus form the Gfh1-like (hydrophobic) and GreA-like (”polar“) interface in both protein families are marked with yellow and green boxes, respectively, whereas the unfavorable substitutions in both Gfh1 and GreA are outlined by red boxes. The potentially functionally crucial segments at the tip of the CC-domains are highlighted with magenta. B, the structure of the Gfh1 protein. The acidic side chains at the CC tip are shown in red. C, the Gfh1 and GreA structures superimposed by the G-domains. D, the CC tips of DksA (green), GreA (yellow), and Gfh1 (cyan). DksA and GreA are superimposed by the CC-domains, and the Gfh1 CC tip is shown in a similar orientation. The hydrogen bonds stabilizing the α-turns in GreA, and DksA are shown as white dashed lines.
Figure 3.
Proposed mechanisms of the Gfh1 action. A and B, the flexibility and the number of the acidic residues at the CC tip of Gfh1 allow for the alternative binding (MG1 or MG2) of the Mg^2+ ions. C, two hypothetical pathways (competitive and noncompetitive) by which the Gfh1 protein may inhibit nucleotide addition. cMg1 and cMg2 are the two catalytic metals, whereas iMg is a putative inhibitory Mg^2+ ion.
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2006, 281, 1309-1312) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21255113 C.E.Blaby-Haas, R.Furman, D.A.Rodionov, I.Artsimovitch, and Crécy-Lagard (2011).
Role of a Zn-independent DksA in Zn homeostasis and stringent response.
  Mol Microbiol, 79, 700-715.  
20639538 A.Sevostyanova, and I.Artsimovitch (2010).
Functional analysis of Thermus thermophilus transcription factor NusG.
  Nucleic Acids Res, 38, 7432-7445.  
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
20459653 Y.Yuzenkova, A.Bochkareva, V.R.Tadigotla, M.Roghanian, S.Zorov, K.Severinov, and N.Zenkin (2010).
Stepwise mechanism for transcription fidelity.
  BMC Biol, 8, 54.  
19896365 D.G.Vassylyev (2009).
Elongation by RNA polymerase: a race through roadblocks.
  Curr Opin Struct Biol, 19, 691-700.  
19489723 E.Nudler (2009).
RNA polymerase active center: the molecular engine of transcription.
  Annu Rev Biochem, 78, 335-361.  
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.  
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.  
18454629 K.Potrykus, and M.Cashel (2008).
(p)ppGpp: still magical?
  Annu Rev Microbiol, 62, 35-51.  
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
17951384 A.Hochschild (2007).
Gene-specific regulation by a transcript cleavage factor: facilitating promoter escape.
  J Bacteriol, 189, 8769-8771.  
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
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
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.  
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.  
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.