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PDBsum entry 1srr

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protein metals Protein-protein interface(s) links
Regulatory protein PDB id
1srr
Jmol
Contents
Protein chains
119 a.a. *
Metals
_CA ×2
Waters ×260
* Residue conservation analysis
PDB id:
1srr
Name: Regulatory protein
Title: Crystal structure of a phosphatase resistant mutant of sporulation response regulator spo0f from bacillus subtilis
Structure: Sporulation response regulatory protein. Chain: a, b, c. Synonym: spo0f. Engineered: yes. Mutation: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: spo0f. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: t7 promoter
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.219     R-free:   0.278
Authors: Madhusudan,J.M.Whiteley,J.A.Hoch,J.Zapf,N.H.Xuong, K.I.Varughese
Key ref:
Madhusudan et al. (1996). Crystal structure of a phosphatase-resistant mutant of sporulation response regulator Spo0F from Bacillus subtilis. Structure, 4, 679-690. PubMed id: 8805550 DOI: 10.1016/S0969-2126(96)00074-3
Date:
10-Apr-96     Release date:   21-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06628  (SP0F_BACSU) -  Sporulation initiation phosphotransferase F
Seq:
Struc:
124 a.a.
119 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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/S0969-2126(96)00074-3 Structure 4:679-690 (1996)
PubMed id: 8805550  
 
 
Crystal structure of a phosphatase-resistant mutant of sporulation response regulator Spo0F from Bacillus subtilis.
Madhusudan, J.Zapf, J.M.Whiteley, J.A.Hoch, N.H.Xuong, K.I.Varughese.
 
  ABSTRACT  
 
BACKGROUND: Spo0F, a phosphotransferase containing an aspartyl pocket, is involved in the signaling pathway (phosphorelay) controlling sporulation in Bacillus subtilis. It belongs to the superfamily of bacterial response regulatory proteins, which are activated upon phosphorylation of an invariant aspartate residue. This phosphorylation is carried out in a divalent cation dependent reaction catalyzed by cognate histidine kinases. Knowledge of the Spo0F structure would provide valuable information that would enable the elucidation of its function as a secondary messenger in a system in which a phosphate is donated from Spo0F to Spo0B, the third of four main proteins that constitute the phosphorelay. RESULTS: We have determined the crystal structure of a Rap phosphatase resistant mutant, Spo0F Tyr13-->Ser, at 1.9 A resolution. The structure was solved by single isomorphous replacement and anomalous scattering techniques. The overall structural fold is (beta/alpha)5 and contains a central beta sheet. The active site of the molecule is formed by three aspartate residues and a lysine residue which come together at the C terminus of the beta sheet. The active site accommodates a calcium ion. CONCLUSIONS: The structural analysis reveals that the overall topology and metal-binding coordination at the active site are similar to those of the bacterial chemotaxis response regulator CheY. Structural differences between Spo0F and CheY in the vicinity of the active site provide an insight into how similar molecular scaffolds can be adapted to perform different biological roles by the alteration of only a few amino acid residues. These differences may contribute to the observed stability of the phosphorylated species of Spo0F, a feature demanded by its role as a secondary messenger within the phosphorelay system which controls sporulation.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Stereoview of the Spo0F Ca^2+-binding site. The backbone atoms are shown in green, aspartate side chains in red, lysine and arginine side chains in blue, glutamine in light blue, the Ca^2+ ion in purple and water molecules in black. Hydrogen bonds and Ca^2+ coordination are depicted by broken lines. The Ca^2+ coordinating distances with the side-chain carboxylate groups of residues Asp11 and Asp54, the main chain peptide carbonyl of Lys56, and the water molecules W1 and W2 are 2.05, 2.33, 2.25, 2.10 and 2.44 å, respectively. Figure 4. Stereoview of the Spo0F Ca^2+-binding site. The backbone atoms are shown in green, aspartate side chains in red, lysine and arginine side chains in blue, glutamine in light blue, the Ca^2+ ion in purple and water molecules in black. Hydrogen bonds and Ca^2+ coordination are depicted by broken lines. The Ca^2+ coordinating distances with the side-chain carboxylate groups of residues Asp11 and Asp54, the main chain peptide carbonyl of Lys56, and the water molecules W1 and W2 are 2.05, 2.33, 2.25, 2.10 and 2.44 å, respectively. (Figure created using SETOR [[3]59].)
Figure 7.
Figure 7. Stereoview of the superposition of E. coli Spo0F (residues 80–121) and the corresponding residues of CheY from S. typhimurium which are shown in yellow and red respectively. The side chains of Thr82 and His101 (of Spo0F) and the side chains of Thr87 and Tyr106 (of CheY) are also shown as ball-and-stick representations [16]. Figure 7. Stereoview of the superposition of E. coli Spo0F (residues 80–121) and the corresponding residues of CheY from S. typhimurium which are shown in yellow and red respectively. The side chains of Thr82 and His101 (of Spo0F) and the side chains of Thr87 and Tyr106 (of CheY) are also shown as ball-and-stick representations [[3]16].
 
  The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 679-690) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20133181 H.Szurmant, and J.A.Hoch (2010).
Interaction fidelity in two-component signaling.
  Curr Opin Microbiol, 13, 190-197.  
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.  
18298828 E.Kolmos, H.Schoof, M.Plümer, and S.J.Davis (2008).
Structural insights into the function of the core-circadian factor TIMING OF CAB2 EXPRESSION 1 (TOC1).
  J Circadian Rhythms, 6, 3.  
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
17559414 H.Tan, F.Janiak-Spens, and A.H.West (2007).
Functional characterization of the phosphorelay protein Mpr1p from Schizosaccharomyces pombe.
  FEMS Yeast Res, 7, 912-921.  
17350627 P.D.McLaughlin, B.G.Bobay, E.J.Regel, R.J.Thompson, J.A.Hoch, and J.Cavanagh (2007).
Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition.
  FEBS Lett, 581, 1425-1429.  
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
17001075 R.Grenha, N.J.Rzechorzek, J.A.Brannigan, R.N.de Jong, E.Ab, T.Diercks, V.Truffault, J.C.Ladds, M.J.Fogg, C.Bongiorni, M.Perego, R.Kaptein, K.S.Wilson, G.E.Folkers, and A.J.Wilkinson (2006).
Structural characterization of Spo0E-like protein-aspartic acid phosphatases that regulate sporulation in bacilli.
  J Biol Chem, 281, 37993-38003.
PDB codes: 2bzb 2c0s
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.  
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.  
15880257 X.H.Cai, Q.Zhang, S.Y.Shi, and D.F.Ding (2005).
Searching for potential drug targets in two-component and phosphorelay signal-transduction systems using three-dimensional cluster analysis.
  Acta Biochim Biophys Sin (Shanghai), 37, 293-302.  
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
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.  
12950917 L.Core, and M.Perego (2003).
TPR-mediated interaction of RapC with ComA inhibits response regulator-DNA binding for competence development in Bacillus subtilis.
  Mol Microbiol, 49, 1509-1522.  
12702718 M.E.Castelli, A.Cauerhff, M.Amongero, F.C.Soncini, and E.G.Vescovi (2003).
The H box-harboring domain is key to the function of the Salmonella enterica PhoQ Mg2+-sensor in the recognition of its partner PhoP.
  J Biol Chem, 278, 23579-23585.  
12191621 K.Stephenson, and J.A.Hoch (2002).
Virulence- and antibiotic resistance-associated two-component signal transduction systems of Gram-positive pathogenic bacteria as targets for antimicrobial therapy.
  Pharmacol Ther, 93, 293-305.  
11872115 N.Browne, and B.C.Dowds (2002).
Acid stress in the food pathogen Bacillus cereus.
  J Appl Microbiol, 92, 404-414.  
12077459 S.Cabantous, V.Guillet, N.Ohta, A.Newton, and J.P.Samama (2002).
Characterization and crystallization of DivK, an essential response regulator for cell division and differentiation in Caulobacter crescentus.
  Acta Crystallogr D Biol Crystallogr, 58, 1249-1251.  
12067336 S.J.Stephenson, and M.Perego (2002).
Interaction surface of the Spo0A response regulator with the Spo0E phosphatase.
  Mol Microbiol, 44, 1455-1467.  
12176983 V.Guillet, N.Ohta, S.Cabantous, A.Newton, and J.P.Samama (2002).
Crystallographic and biochemical studies of DivK reveal novel features of an essential response regulator in Caulobacter crescentus.
  J Biol Chem, 277, 42003-42010.
PDB codes: 1m5t 1m5u 1mav 1mb0 1mb3
10966457 A.M.Stock, V.L.Robinson, and P.N.Goudreau (2000).
Two-component signal transduction.
  Annu Rev Biochem, 69, 183-215.  
10781554 T.Schiött, and L.Hederstedt (2000).
Efficient spore synthesis in Bacillus subtilis depends on the CcdA protein.
  J Bacteriol, 182, 2845-2854.  
11053847 Y.J.Im, C.M.Park, J.I.Kim, S.S.Yang, J.G.Kang, S.H.Rho, J.I.Kim, W.K.Song, P.S.Song, and S.H.Eom (2000).
Crystallization and preliminary X-ray crystallographic studies of response regulator for cyanobacterial phytochrome, Rcp1.
  Acta Crystallogr D Biol Crystallogr, 56, 1446-1448.  
  10390224 J.J.Hilliard, R.M.Goldschmidt, L.Licata, E.Z.Baum, and K.Bush (1999).
Multiple mechanisms of action for inhibitors of histidine protein kinases from bacterial two-component systems.
  Antimicrob Agents Chemother, 43, 1693-1699.  
10089466 K.Muchová, R.J.Lewis, J.A.Brannigan, W.A.Offen, D.P.Brown, I.Barák, P.Youngman, and A.J.Wilkinson (1999).
Crystallization of the regulatory and effector domains of the key sporulation response regulator Spo0A.
  Acta Crystallogr D Biol Crystallogr, 55, 671-676.  
10393292 M.Kato, T.Shimizu, T.Mizuno, and T.Hakoshima (1999).
Structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor protein ArcB complexed with the chemotaxis response regulator CheY.
  Acta Crystallogr D Biol Crystallogr, 55, 1257-1263.
PDB code: 1bdj
10089538 M.Sol, F.Gomis-Rüth, A.Guasch, L.Serrano, and M.Coll (1998).
Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of the receiver domain of PhoB.
  Acta Crystallogr D Biol Crystallogr, 54, 1460-1463.  
9465023 S.Djordjevic, P.N.Goudreau, Q.Xu, A.M.Stock, and A.H.West (1998).
Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain.
  Proc Natl Acad Sci U S A, 95, 1381-1386.
PDB code: 1a2o
9335530 M.Madhusudan, J.Zapf, J.A.Hoch, J.M.Whiteley, N.H.Xuong, and K.I.Varughese (1997).
A response regulatory protein with the site of phosphorylation blocked by an arginine interaction: crystal structure of Spo0F from Bacillus subtilis.
  Biochemistry, 36, 12739-12745.
PDB code: 1nat
9254596 V.A.Feher, J.W.Zapf, J.A.Hoch, J.M.Whiteley, L.P.McIntosh, M.Rance, N.J.Skelton, F.W.Dahlquist, and J.Cavanagh (1997).
High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, Spo0F: implications for phosphorylation and molecular recognition.
  Biochemistry, 36, 10015-10025.
PDB codes: 1fsp 2fsp
9141138 X.Z.Zhou, Madhusudan, J.M.Whiteley, J.A.Hoch, and K.I.Varughese (1997).
Purification and preliminary crystallographic studies on the sporulation response regulatory phosphotransferase protein, Spo0B, from Bacillus subtilis.
  Proteins, 27, 597-600.  
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.