PDBsum entry 3ihq

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Transcription/transferase PDB id
Protein chains
115 a.a. *
67 a.a. *
Waters ×39
* Residue conservation analysis
PDB id:
Name: Transcription/transferase
Title: Crystal structure of reduced c10s spx in complex with the alpha c-terminal domain of RNA polymeras
Structure: Regulatory protein spx. Chain: a. Engineered: yes. Mutation: yes. DNA-directed RNA polymerase subunit alpha. Chain: b. Fragment: unp residues 245-314. Synonym: rnap subunit alpha, transcriptase subunit alpha, RNA polymerase subunit alpha.
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: bsu11500, spxa. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: bsu01430, rpoa.
1.90Å     R-factor:   0.236     R-free:   0.278
Authors: K.J.Newberry,R.G.Brennan
Key ref: M.M.Nakano et al. (2010). Promoter recognition by a complex of Spx and the C-terminal domain of the RNA polymerase alpha subunit. PLoS One, 5, e8664. PubMed id: 20084284
30-Jul-09     Release date:   02-Feb-10    
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Protein chain
Pfam   ArchSchema ?
O31602  (SPX_BACSU) -  Regulatory protein Spx
131 a.a.
115 a.a.*
Protein chain
No UniProt id for this chain
Struc: 67 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     transcription, DNA-dependent   3 terms 
  Biochemical function     protein binding     3 terms  


PLoS One 5:e8664 (2010)
PubMed id: 20084284  
M.M.Nakano, A.Lin, C.S.Zuber, K.J.Newberry, R.G.Brennan, P.Zuber.
BACKGROUND: Spx, an ArsC (arsenate reductase) family member, is a global transcriptional regulator of the microbial stress response and is highly conserved amongst Gram-positive bacteria. Bacillus subtilis Spx protein exerts positive and negative control of transcription through its interaction with the C-terminal domain of the RNA polymerase (RNAP) alpha subunit (alphaCTD). Spx activates trxA (thioredoxin) and trxB (thioredoxin reductase) in response to thiol stress, and bears an N-terminal C10XXC13 redox disulfide center that is oxidized in active Spx. METHODOLOGY/PRINCIPAL FINDINGS: The structure of mutant Spx(C10S) showed a change in the conformation of helix alpha4. Amino acid substitutions R60E and K62E within and adjacent to helix alpha4 conferred defects in Spx-activated transcription but not Spx-dependent repression. Electrophoretic mobility-shift assays showed alphaCTD interaction with trxB promoter DNA, but addition of Spx generated a supershifted complex that was disrupted in the presence of reductant (DTT). Interaction of alphaCTD/Spx complex with promoter DNA required the cis-acting elements -45AGCA-42 and -34AGCG-31 of the trxB promoter. The Spx(G52R) mutant, defective in alphaCTD binding, did not interact with the alphaCTD-trxB complex. Spx(R60E) not only failed to complex with alphaCTD-trxB, but also disrupted alphaCTD-trxB DNA interaction. CONCLUSIONS/SIGNIFICANCE: The results show that Spx and alphaCTD form a complex that recognizes the promoter DNA of an Spx-controlled gene. A conformational change during oxidation of Spx to the disulfide form likely alters the structure of Spx alpha helix alpha4, which contains residues that function in transcriptional activation and alphaCTD/Spx-promoter interaction. The results suggest that one of these residues, R60 of the alpha4 region of oxidized Spx, functions in alphaCTD/Spx-promoter contact but not in alphaCTD interaction.

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.  