PDBsum entry 3gfk

Go to PDB code: 
protein Protein-protein interface(s) links
Transcription/transferase PDB id
Protein chains
118 a.a. *
76 a.a. *
Waters ×257
* Residue conservation analysis
PDB id:
Name: Transcription/transferase
Title: Crystal structure of bacillus subtilis spx/RNA polymerase alpha subunit c-terminal domain complex
Structure: Regulatory protein spx. Chain: a. Engineered: yes. DNA-directed RNA polymerase subunit alpha. Chain: b. Fragment: alpha c-terminal domain (alpha-ctd). Synonym: rnap subunit alpha, transcriptase subunit alpha, RNA polymerase subunit alpha. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: spxa, bsu11500. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rpoa, bsu01430. Expression_system_taxid: 562
2.30Å     R-factor:   0.229     R-free:   0.282
Authors: V.Lamour,L.F.Westblade,E.A.Campbell,S.A.Darst
Key ref: V.Lamour et al. (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. PubMed id: 19580872
27-Feb-09     Release date:   10-Mar-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O31602  (SPX_BACSU) -  Regulatory protein Spx
131 a.a.
118 a.a.
Protein chain
Pfam   ArchSchema ?
P20429  (RPOA_BACSU) -  DNA-directed RNA polymerase subunit alpha
314 a.a.
76 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 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   3 terms 
  Biochemical function     protein binding     3 terms  


J Struct Biol 168:352-356 (2009)
PubMed id: 19580872  
Crystal structure of the in vivo-assembled Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex.
V.Lamour, L.F.Westblade, E.A.Campbell, S.A.Darst.
The Bacillus subtilis Spx protein is a global transcription factor that interacts with the C-terminal domain of the RNA polymerase alpha subunit (alphaCTD) and regulates transcription of genes involved in thiol-oxidative stress, sporulation, competence, and organosulfur metabolism. Here we determined the X-ray crystal structure of the Spx/alphaCTD complex from an entirely new crystal form than previously reported [Newberry, K.J., Nakano, S., Zuber, P., Brennan, R.G., 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. USA 102, 15839-15844]. Comparison of the previously reported sulfate-bound complex and our sulfate-free complex reveals subtle conformational changes that may be important for the role of Spx in regulating organosulfur metabolism.

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.  
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
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.