PDBsum entry 1z3e

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protein ligands Protein-protein interface(s) links
Transcription PDB id
Jmol PyMol
Protein chains
119 a.a. *
67 a.a. *
SO4 ×4
Waters ×143
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Crystal structure of spx in complex with thE C-terminal domain of the RNA polymerase alpha subunit
Structure: Regulatory protein spx. Chain: a. Fragment: transcription regulator. Engineered: yes. DNA-directed RNA polymerase alpha chain. Chain: b. Fragment: c-terminal domain of RNA polymerase alpha subunit. Synonym: rnap alpha subunit, transcriptase alpha chain,
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: spxa. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: rpoa.
1.50Å     R-factor:   0.196     R-free:   0.220
Authors: K.J.Newberry,S.Nakano,P.Zuber,R.G.Brennan
Key ref:
K.J.Newberry et al. (2005). Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase. Proc Natl Acad Sci U S A, 102, 15839-15844. PubMed id: 16249335 DOI: 10.1073/pnas.0506592102
11-Mar-05     Release date:   11-Oct-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O31602  (SPX_BACSU) -  Regulatory protein Spx
131 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P20429  (RPOA_BACSU) -  DNA-directed RNA polymerase subunit alpha
314 a.a.
67 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain B: 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!
  Cellular component     cytoplasm   1 term 
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     protein binding     3 terms  


DOI no: 10.1073/pnas.0506592102 Proc Natl Acad Sci U S A 102:15839-15844 (2005)
PubMed id: 16249335  
Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase.
K.J.Newberry, S.Nakano, P.Zuber, R.G.Brennan.
Spx, a global transcription regulator in Bacillus subtilis, interacts with the C-terminal domain of the alpha subunit (alphaCTD) of RNA polymerase to control gene expression under conditions of disulfide stress, which is sensed by disulfide bond formation between Spx residues C10 and C13. Here, we describe the crystal structure of the B. subtilis alphaCTD bound to oxidized Spx. Analysis of the complex reveals interactions between three regions of "anti-alpha" Spx and helix alpha1 and the "261" determinant of alphaCTD. The former contact could disrupt the interaction between alphaCTD and activator proteins or alter the DNA-bound conformation of alphaCTD, thereby repressing activator-stimulated transcription. Binding to the 261 determinant would prevent interaction between alphaCTD and region 4 of sigma(A). Intriguingly, the Spx disulfide bond is far from the alphaCTD-Spx interface, suggesting that Spx regulates transcription allosterically or through the redox-dependent creation or destruction of binding sites for additional components of the transcription machinery.
  Selected figure(s)  
Figure 2.
Fig. 2. Disulfide bridge and sulfate binding sites of oxidized Spx. (A) The disulfide bridge is shown as yellow sticks. The sulfate, which is found in both Spx and ArsC, and may be involved in transcription regulation by Spx, is bound by the guanidinium moiety of residue R92 and the main chain carbonyl oxygen of S12. A second sulfate ion, which is found only in the Spx- CTD structure, is shown to the left of R92. Interactions between the sulfates and protein are depicted by dashed line. (B) A representative 2F[o] - F[c] simulated annealing composite omit map contoured at 1 shows the electron density for the disulfide bridge of Spx.
Figure 3.
Fig. 3. The Spx- CTD heterodimer interface. (A and B) Hydrogen bonding interactions at the dimer interface. The backbones of Spx and CTD are colored pink and green, respectively. Interacting residues are depicted as sticks and are colored according to atom type. Hydrogen bonds are depicted as dashes. (C) Interactions of cxs mutants of CTD (V260 and Y263) and Spx (G52). These residues cluster and are shown as blue sticks.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20626317 H.Antelmann, and J.D.Helmann (2011).
Thiol-based redox switches and gene regulation.
  Antioxid Redox Signal, 14, 1049-1063.  
20711169 D.Xu, P.Muniandy, E.Leo, J.Yin, S.Thangavel, X.Shen, M.Ii, K.Agama, R.Guo, D.Fox, A.R.Meetei, L.Wilson, H.Nguyen, N.P.Weng, S.J.Brill, L.Li, A.Vindigni, Y.Pommier, M.Seidman, and W.Wang (2010).
Rif1 provides a new DNA-binding interface for the Bloom syndrome complex to maintain normal replication.
  EMBO J, 29, 3140-3155.  
20598080 H.Yang, G.L.Lipscomb, A.M.Keese, G.J.Schut, M.Thomm, M.W.Adams, B.C.Wang, and R.A.Scott (2010).
SurR regulates hydrogen production in Pyrococcus furiosus by a sulfur-dependent redox switch.
  Mol Microbiol, 77, 1111-1122.  
20233935 J.K.Kajfasz, I.Rivera-Ramos, J.Abranches, A.R.Martinez, P.L.Rosalen, A.M.Derr, R.G.Quivey, and J.A.Lemos (2010).
Two Spx proteins modulate stress tolerance, survival, and virulence in Streptococcus mutans.
  J Bacteriol, 192, 2546-2556.  
20084284 M.M.Nakano, A.Lin, C.S.Zuber, K.J.Newberry, R.G.Brennan, and P.Zuber (2010).
Promoter recognition by a complex of Spx and the C-terminal domain of the RNA polymerase alpha subunit.
  PLoS One, 5, e8664.
PDB code: 3ihq
19627499 C.Turlan, M.Prudhomme, G.Fichant, B.Martin, and C.Gutierrez (2009).
SpxA1, a novel transcriptional regulator involved in X-state (competence) development in Streptococcus pneumoniae.
  Mol Microbiol, 73, 492-506.  
19575568 P.Zuber (2009).
Management of oxidative stress in Bacillus.
  Annu Rev Microbiol, 63, 575-597.  
19074380 S.K.Garg, S.Kommineni, L.Henslee, Y.Zhang, and P.Zuber (2009).
The YjbH protein of Bacillus subtilis enhances ClpXP-catalyzed proteolysis of Spx.
  J Bacteriol, 191, 1268-1277.  
19580872 V.Lamour, L.F.Westblade, E.A.Campbell, and S.A.Darst (2009).
Crystal structure of the in vivo-assembled Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex.
  J Struct Biol, 168, 352-356.
PDB code: 3gfk
18643936 A.Reder, D.Höper, C.Weinberg, U.Gerth, M.Fraunholz, and M.Hecker (2008).
The Spx paralogue MgsR (YqgZ) controls a subregulon within the general stress response of Bacillus subtilis.
  Mol Microbiol, 69, 1104-1120.  
18687074 D.Y.Reyes, and P.Zuber (2008).
Activation of transcription initiation by Spx: formation of transcription complex and identification of a Cis-acting element required for transcriptional activation.
  Mol Microbiol, 69, 765-779.  
19019158 L.E.Bingle, K.V.Rajasekar, S.Muntaha, V.Nadella, E.I.Hyde, and C.M.Thomas (2008).
A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co-regulator KorB.
  Mol Microbiol, 70, 1502-1514.  
17189364 H.Geng, Y.Zhu, K.Mullen, C.S.Zuber, and M.M.Nakano (2007).
Characterization of ResDE-dependent fnr transcription in Bacillus subtilis.
  J Bacteriol, 189, 1745-1755.  
17908206 J.T.Larsson, A.Rogstam, and C.von Wachenfeldt (2007).
YjbH is a novel negative effector of the disulphide stress regulator, Spx, in Bacillus subtilis.
  Mol Microbiol, 66, 669-684.  
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.  
17158660 M.Leelakriangsak, K.Kobayashi, and P.Zuber (2007).
Dual negative control of spx transcription initiation from the P3 promoter by repressors PerR and YodB in Bacillus subtilis.
  J Bacteriol, 189, 1736-1744.  
17158663 M.Leelakriangsak, and P.Zuber (2007).
Transcription from the P3 promoter of the Bacillus subtilis spx gene is induced in response to disulfide stress.
  J Bacteriol, 189, 1727-1735.  
16885442 S.Y.Choi, D.Reyes, M.Leelakriangsak, and P.Zuber (2006).
The global regulator Spx functions in the control of organosulfur metabolism in Bacillus subtilis.
  J Bacteriol, 188, 5741-5751.  
16740936 Y.Zhang, S.Nakano, S.Y.Choi, and P.Zuber (2006).
Mutational analysis of the Bacillus subtilis RNA polymerase alpha C-terminal domain supports the interference model of Spx-dependent repression.
  J Bacteriol, 188, 4300-4311.  
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.