PDBsum entry 1pux

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protein links
Transferase PDB id
Protein chain
124 a.a. *
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Nmr solution structure of bef3-activated spo0f, 20 conformers
Structure: Sporulation initiation phosphotransferase f. Chain: a. Synonym: stage 0 sporulation protein f. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: spo0f. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: A.K.Gardino,B.F.Volkman,H.S.Cho,S.Y.Lee,D.E.Wemmer,D.Kern
Key ref:
A.K.Gardino et al. (2003). The NMR solution structure of BeF(3)(-)-activated Spo0F reveals the conformational switch in a phosphorelay system. J Mol Biol, 331, 245-254. PubMed id: 12875849 DOI: 10.1016/S0022-2836(03)00733-2
25-Jun-03     Release date:   19-Aug-03    
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Protein chain
Pfam   ArchSchema ?
P06628  (SP0F_BACSU) -  Sporulation initiation phosphotransferase F
124 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     intracellular signal transduction   4 terms 
  Biochemical function     protein binding     5 terms  


DOI no: 10.1016/S0022-2836(03)00733-2 J Mol Biol 331:245-254 (2003)
PubMed id: 12875849  
The NMR solution structure of BeF(3)(-)-activated Spo0F reveals the conformational switch in a phosphorelay system.
A.K.Gardino, B.F.Volkman, H.S.Cho, S.Y.Lee, D.E.Wemmer, D.Kern.
Two-component systems, which are comprised of a single histidine-aspartate phosphotransfer module, are the dominant signaling pathways in bacteria and have recently been identified in several eukaryotic organisms as well. A tandem connection of two or more histidine-aspartate motifs forms complex phosphorelays. While response regulators from simple two-component systems have been characterized structurally in their inactive and active forms, we address here the question of whether a response regulator from a phosphorelay has a distinct structural basis of activation. We report the NMR solution structure of BeF(3)(-)-activated Spo0F, the first structure of a response regulator from a phosphorelay in its activated state. Conformational changes were found in regions previously identified to change in simple two-component systems. In addition, a downward shift by half a helical turn in helix 1, located on the opposite side of the common activation surface, was observed as a consequence of BeF(3)(-) activation. Conformational changes in helix 1 can be rationalized by the distinct function of phosphoryl transfer to the second histidine kinase, Spo0B, because helix 1 is known to interact directly with Spo0B and the phosphatase RapB. The identification of structural rearrangements in Spo0F supports the hypothesis of a pre-existing equilibrium between the inactive and active state prior to phosphorylation that was suggested on the basis of previous NMR dynamics studies on Spo0F. A shift of a pre-existing equilibrium is likely a general feature of response regulators.
  Selected figure(s)  
Figure 3.
Figure 3. Comparison of inactive versus active structures of receiver domains among various response regulators. Inactive forms are colored in blue and active forms are colored in orange for: (A) CheY; (B) NtrC; (C) DctD; and (D) FixJ. Regions of the protein previously determined not to change in structure upon activation were used for superposition as follows: CheY: 8-11, 15-26, 33-34, 39-46, and 53-56, RMSD=0.85; NtrC: 4-9, 14-53, and 108-121, RMSD=1.74; FixJ: 5-8, 16-47, 49-52, 107-120, RMSD=0.31; DctD: 6-10, 14-26, 30-34, 37-42, 51-55, 63-73, RMSD=0.3. PDB accession codes for all structures shown are as follows: 3CHY (inactive CheY), 1DJM (BeF[3]^ --CheY), 1DC7 (inactive NtrC), 1DC8 (P-NtrC), 1DBW (inactive FixJ), 1D5W (P-FixJ), 1QKK (inactive DctD), and 1L5Y (BeF[3]^ --DctD).
Figure 4.
Figure 4. Molecular recognition in Spo0F. (A) The direct phosphorelay partner, Spo0B, is displayed according to the X-ray co-crystal structure of Spo0F (green) and Spo0B (gray) (1F51);[28] the side-chains of the phosphorelay residues Asp54 in Spo0F and His30 in Spo0B are highlighted in purple. The other partners, KinA and RapB, are represented symbolically due to lack of structural information. Residues implicated in protein-protein interactions between Spo0F and its interaction partners colored in red were found via alanine-scanning mutagenesis[31]: 12, 13, 14, 15, 16, 18, 19, 21, 34, 35, 37, 38, 56, 57, 58, 59, 81, 83, 84, 85, 86, 87, 104, 105, 106, 107, and 108. Superposition of Spo0F from the co-crystal complex (green) and (B) inactive Spo0F (blue) or (C) BeF[3]^ --Spo0F (orange) suggests that Spo0F was crystallized in its inactive conformation in complex with Spo0B. Regions of superposition for each pair of structures are residues 5-9, 29-33, 36-45, 50-53, and 108-118.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 245-254) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20702407 C.M.Barbieri, T.R.Mack, V.L.Robinson, M.T.Miller, and A.M.Stock (2010).
Regulation of response regulator autophosphorylation through interdomain contacts.
  J Biol Chem, 285, 32325-32335.
PDB codes: 3nhz 3nnn 3nns
20226790 R.D.Hills, S.V.Kathuria, L.A.Wallace, I.J.Day, C.L.Brooks, and C.R.Matthews (2010).
Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins.
  J Mol Biol, 398, 332-350.  
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
18557815 S.A.Thomas, J.A.Brewster, and R.B.Bourret (2008).
Two variable active site residues modulate response regulator phosphoryl group stability.
  Mol Microbiol, 69, 453-465.  
18682221 V.Z.Miloushev, F.Bahna, C.Ciatto, G.Ahlsen, B.Honig, L.Shapiro, and A.G.Palmer (2008).
Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins.
  Structure, 16, 1195-1205.  
18076904 X.Zhao, D.M.Copeland, A.S.Soares, and A.H.West (2008).
Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog.
  J Mol Biol, 375, 1141-1151.
PDB code: 2r25
17616594 M.K.Matta, E.E.Lioliou, C.H.Panagiotidis, D.A.Kyriakidis, and C.A.Panagiotidis (2007).
Interactions of the antizyme AtoC with regulatory elements of the Escherichia coli atoDAEB operon.
  J Bacteriol, 189, 6324-6332.  
16434396 E.Nowak, S.Panjikar, P.Konarev, D.I.Svergun, and P.A.Tucker (2006).
The structural basis of signal transduction for the response regulator PrrA from Mycobacterium tuberculosis.
  J Biol Chem, 281, 9659-9666.  
16788205 K.I.Varughese, I.Tsigelny, and H.Zhao (2006).
The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state.
  J Bacteriol, 188, 4970-4977.
PDB code: 2ftk
16816192 R.Gao, A.Mukhopadhyay, F.Fang, and D.G.Lynn (2006).
Constitutive activation of two-component response regulators: characterization of VirG activation in Agrobacterium tumefaciens.
  J Bacteriol, 188, 5204-5211.  
16321925 D.E.Wemmer, and D.Kern (2005).
Beryllofluoride binding mimics phosphorylation of aspartate in response regulators.
  J Bacteriol, 187, 8229-8230.  
16333746 D.J.Kojetin, R.J.Thompson, L.M.Benson, S.Naylor, J.Waterman, K.G.Davies, C.H.Opperman, K.Stephenson, J.A.Hoch, and J.Cavanagh (2005).
Structural analysis of divalent metals binding to the Bacillus subtilis response regulator Spo0F: the possibility for in vitro metalloregulation in the initiation of sporulation.
  Biometals, 18, 449-466.  
16321923 K.I.Varughese (2005).
Conformational changes of Spo0F along the phosphotransfer pathway.
  J Bacteriol, 187, 8221-8227.  
16321926 K.I.Varughese (2005).
Rebuttal: beryllofluoride binding mimics phosphorylation of aspartate in response regulators.
  J Bacteriol, 187, 8231.  
16154092 P.Bachhawat, G.V.Swapna, G.T.Montelione, and A.M.Stock (2005).
Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states.
  Structure, 13, 1353-1363.
PDB code: 1zes
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
15039551 D.Mukhopadhyay, U.Sen, J.Zapf, and K.I.Varughese (2004).
Metals in the sporulation phosphorelay: manganese binding by the response regulator Spo0F.
  Acta Crystallogr D Biol Crystallogr, 60, 638-645.
PDB code: 1pey
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.  
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.