PDBsum entry 1dz3

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Response regulator PDB id
Jmol PyMol
Protein chain
123 a.a. *
Waters ×95
* Residue conservation analysis
PDB id:
Name: Response regulator
Title: Domain-swapping in the sporulation response regulator spo0a
Structure: Stage 0 sporulation protein a. Chain: a. Fragment: receiver domain. Engineered: yes
Source: Bacillus stearothermophilus. Organism_taxid: 1422. Cellular_location: cytoplasm. Gene: spo0a. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.65Å     R-factor:   0.235     R-free:   0.265
Authors: R.J.Lewis,J.A.Brannigan,K.Muchova,G.Leonard,I.Barak, A.J.Wilkinson
Key ref:
R.J.Lewis et al. (2000). Domain swapping in the sporulation response regulator Spo0A. J Mol Biol, 297, 757-770. PubMed id: 10731426 DOI: 10.1006/jmbi.2000.3598
15-Feb-00     Release date:   10-Apr-00    
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Protein chain
Pfam   ArchSchema ?
P52934  (SP0A_GEOSE) -  Stage 0 sporulation protein A
259 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     two-component signal transduction system (phosphorelay)   1 term 


DOI no: 10.1006/jmbi.2000.3598 J Mol Biol 297:757-770 (2000)
PubMed id: 10731426  
Domain swapping in the sporulation response regulator Spo0A.
R.J.Lewis, K.Muchová, J.A.Brannigan, I.Barák, G.Leonard, A.J.Wilkinson.
Adaptive responses of micro-organisms, such as chemotaxis and sporulation, are governed by two-component systems consisting of sensor kinases, that interpret environmental signals, and response regulators which activate the appropriate physiological responses. Signal transduction via response regulator proteins is mediated through transient phosphorylation of aspartic acid residues. In Spo0A, the key regulator of development (sporulation) in Bacillus, phosphorylation of the N-terminal receiver domain (N-Spo0A) at aspartate-55 switches on the transcription activation functions residing in the C-terminal effector domain. Here we report the crystal structure of N-Spo0A from Bacillus stearothermophilus at 1.6 A spacing, revealing a dimer formed by an alpha-helix swap. Comparison of this structure with the recently described structure of phosphorylated N-Spo0A shows that dimer formation results from a cis-trans isomerization of the Lys106--Pro107 peptide bond. The quaternary reorganization is associated with alterations in the active site stereochemistry which may have implications for signalling. Remarkably, this 3-D domain swapped N-Spo0A dimer has an identical topology to a hypothetical CheY-like dimer, recently proposed as an intermediate in the evolution of the family of periplasmic substrate binding proteins.
  Selected figure(s)  
Figure 2.
Figure 2. (a) Ribbon and (b) space filling representations of the N-Spo0A dimer. One protomer is coloured red, the other green. The side-chains of Lys106 and Asp55 are in dark blue.
Figure 3.
Figure 3. Stereo view of a comparative C^a trace of the N-Spo0A vert, similar P monomeric structure coloured in blue and the N-Spo0A dimer coloured in green for molecule 1 (residues 2-108) and red for molecule 2 (helix a5, residues 108-122). The view is looking down onto the active site with the aspartyl-phosphate and the calcium ion of N-Spo0A vert, similar P drawn as ball-and-stick models. The structures were superimposed by least-squares minimization procedures applied to the C^a atoms of residues 2-100 of molecule 1 and 112-123 of molecule 2 from N-Spo0A, and residues 2-100 and 112-123 from one molecule of N-Spo0A vert, similar P.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 757-770) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
18045868 A.R.Diaz, S.Stephenson, J.M.Green, V.M.Levdikov, A.J.Wilkinson, and M.Perego (2008).
Functional Role for a Conserved Aspartate in the Spo0E Signature Motif Involved in the Dephosphorylation of the Bacillus subtilis Sporulation Regulator Spo0A.
  J Biol Chem, 283, 2962-2972.  
18353359 G.Wisedchaisri, M.Wu, D.R.Sherman, and W.G.Hol (2008).
Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation.
  J Mol Biol, 378, 227-242.
PDB codes: 3c3w 3c57
17942407 J.King-Scott, E.Nowak, E.Mylonas, S.Panjikar, M.Roessle, D.I.Svergun, and P.A.Tucker (2007).
The structure of a full-length response regulator from Mycobacterium tuberculosis in a stabilized three-dimensional domain-swapped, activated state.
  J Biol Chem, 282, 37717-37729.
PDB code: 2oqr
17322531 T.Gao, X.Zhang, N.B.Ivleva, S.S.Golden, and A.LiWang (2007).
NMR structure of the pseudo-receiver domain of CikA.
  Protein Sci, 16, 465-475.
PDB code: 2j48
16281059 H.Makyio, R.Iino, C.Ikeda, H.Imamura, M.Tamakoshi, M.Iwata, D.Stock, R.A.Bernal, E.P.Carpenter, M.Yoshida, K.Yokoyama, and S.Iwata (2005).
Structure of a central stalk subunit F of prokaryotic V-type ATPase/synthase from Thermus thermophilus.
  EMBO J, 24, 3974-3983.
PDB code: 2d00
15659154 I.Barák, E.Ricca, and S.M.Cutting (2005).
From fundamental studies of sporulation to applied spore research.
  Mol Microbiol, 55, 330-338.  
15808745 K.Stephenson, and R.J.Lewis (2005).
Molecular insights into the initiation of sporulation in Gram-positive bacteria: new technologies for an old phenomenon.
  FEMS Microbiol Rev, 29, 281-301.  
15090529 C.J.Bent, N.W.Isaacs, T.J.Mitchell, and A.Riboldi-Tunnicliffe (2004).
Crystal structure of the response regulator 02 receiver domain, the essential YycF two-component system of Streptococcus pneumoniae in both complexed and native states.
  J Bacteriol, 186, 2872-2879.
PDB codes: 1nxo 1nxp 1nxt 1nxw
15028686 H.Geng, S.Nakano, and M.M.Nakano (2004).
Transcriptional activation by Bacillus subtilis ResD: tandem binding to target elements and phosphorylation-dependent and -independent transcriptional activation.
  J Bacteriol, 186, 2028-2037.  
15255896 K.Muchová, R.J.Lewis, D.Perecko, J.A.Brannigan, J.C.Ladds, A.Leech, A.J.Wilkinson, and I.Barák (2004).
Dimer-induced signal propagation in Spo0A.
  Mol Microbiol, 53, 829-842.  
12486062 C.Birck, Y.Chen, F.M.Hulett, and J.P.Samama (2003).
The crystal structure of the phosphorylation domain in PhoP reveals a functional tandem association mediated by an asymmetric interface.
  J Bacteriol, 185, 254-261.
PDB code: 1mvo
14627822 J.Liu, K.Tan, and G.D.Stormo (2003).
Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria.
  Nucleic Acids Res, 31, 6891-6903.  
12951249 J.R.Trotter, and A.H.Bishop (2003).
Phylogenetic analysis and confirmation of the endospore-forming nature of Pasteuria penetrans based on the spo0A gene.
  FEMS Microbiol Lett, 225, 249-256.  
12675798 K.Saito, E.Ito, K.Hosono, K.Nakamura, K.Imai, T.Iizuka, Y.Shiro, and H.Nakamura (2003).
The uncoupling of oxygen sensing, phosphorylation signalling and transcriptional activation in oxygen sensor FixL and FixJ mutants.
  Mol Microbiol, 48, 373-383.  
12176382 H.Zhao, T.Msadek, J.Zapf, Madhusudan, J.A.Hoch, and K.I.Varughese (2002).
DNA complexed structure of the key transcription factor initiating development in sporulating bacteria.
  Structure, 10, 1041-1050.
PDB code: 1lq1
12406209 K.Stephenson, and J.A.Hoch (2002).
Evolution of signalling in the sporulation phosphorelay.
  Mol Microbiol, 46, 297-304.  
12381845 P.Roche, L.Mouawad, D.Perahia, J.P.Samama, and D.Kahn (2002).
Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101.
  Protein Sci, 11, 2622-2630.  
12067336 S.J.Stephenson, and M.Perego (2002).
Interaction surface of the Spo0A response regulator with the Spo0E phosphatase.
  Mol Microbiol, 44, 1455-1467.  
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
11121774 A.L.Sonenshein (2000).
Control of sporulation initiation in Bacillus subtilis.
  Curr Opin Microbiol, 3, 561-566.  
11069648 R.J.Lewis, S.Krzywda, J.A.Brannigan, J.P.Turkenburg, K.Muchová, E.J.Dodson, I.Barák, and A.J.Wilkinson (2000).
The trans-activation domain of the sporulation response regulator Spo0A revealed by X-ray crystallography.
  Mol Microbiol, 38, 198-212.
PDB code: 1fc3
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.