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PDBsum entry 1qmp

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protein metals Protein-protein interface(s) links
Replication PDB id
1qmp
Jmol
Contents
Protein chains
126 a.a. *
Metals
_CA ×4
Waters ×385
* Residue conservation analysis
PDB id:
1qmp
Name: Replication
Title: Phosphorylated aspartate in the crystal structure of the sporulation response regulator, spo0a
Structure: Spo0a. Chain: a, b, c, d. Fragment: receiver domain. Engineered: yes. Other_details: phosphorylated aspartic acid residue 55
Source: Bacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escerichia coli.
Resolution:
2.00Å     R-factor:   0.200     R-free:   0.253
Authors: R.J.Lewis,J.A.Brannigan,K.Muchova,I.Barak,A.J.Wilkinson
Key ref:
R.J.Lewis et al. (1999). Phosphorylated aspartate in the structure of a response regulator protein. J Mol Biol, 294, 9. PubMed id: 10556024 DOI: 10.1006/jmbi.1999.3261
Date:
04-Oct-99     Release date:   14-Nov-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P52934  (SP0A_GEOSE) -  Stage 0 sporulation protein A
Seq:
Struc:
259 a.a.
126 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!
  Biological process     two-component signal transduction system (phosphorelay)   1 term 

 

 
DOI no: 10.1006/jmbi.1999.3261 J Mol Biol 294:9 (1999)
PubMed id: 10556024  
 
 
Phosphorylated aspartate in the structure of a response regulator protein.
R.J.Lewis, J.A.Brannigan, K.Muchová, I.Barák, A.J.Wilkinson.
 
  ABSTRACT  
 
Phosphorylation of aspartic acid residues is the hallmark of two- component signal transduction systems that orchestrate the adaptive responses of micro-organisms to changes in their surroundings. Two-component systems consist of a sensor kinase that interprets environmental signals and a response regulator that activates the appropriate physiological response. Although structures of response regulators are known, little is understood about their activated phosphorylated forms, due to the intrinsic instability of the acid phosphate linkage. Here, we report the phosphorylated structure of the receiver/phosphoacceptor domain of Spo0A, the master regulator of sporulation, from Bacillus stearothermophilus. The phosphoryl group is covalently bonded to the invariant aspartate 55, and co-ordinated to a nearby divalent metal cation, with both species fulfilling their electrostatic potential through interactions with solvent water molecules, the protein main chain, and with side-chains of amino acid residues strongly conserved across the response regulator family. This is the first direct visualisation of a phosphoryl group covalently linked to an aspartic acid residue in any protein, with implications for signalling within the response regulator family.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The active site of N-Spo0A ~ phosphate. (a) Stereo view of the initial electron density map displayed on selected atoms from the final refined model in the vicinity of the aspartyl phosphate (left). The map is calculated using coefficients 2Fobs - Fcalc using 4-fold non-crystallographic symmetry-averaged density modified phases from the initial molecular replacement solution. In these unbiased maps, electron density defining the phosphoryl group, the calcium ion (green) and neighbouring water molecules is clear. (b) Stereo view of an Fobs - Fcalc electron density omit map con- toured at 3.5s displayed around Asp55, the phosphoryl group and the calcium ion in the refined co-ordinate set. This map was calculated with the occupancies of the side-chain atoms of residue 55, the calcium ion and the nearby water molecules set to zero. Atoms are coloured according to type; C (cyan), O (red), N (blue), P (yellow), Ca (grey) and water (green). (c) Stereo view orthogonal to (b). Hydrogen bonds are shown as broken lines, AP denotes the phosphorylated Asp. The calcium ion is seven co-ordinate, its ligands being three water molecules, carboxylate oxygen atoms of Asp10 and Asp55, a phosphoryl oxygen atom and the main-chain carbonyl oxygen atoms of Ile57. The phosphoryl oxygen
Figure 3.
Figure 3. Concerted movements of active site Thr and aromatic side-chains on phosphorylation. (a) Compari- son of the active sites of N-Spo0A ~ phosphate (cyan with phosphorus in yellow), Spo0F (green) and CheY (pink). Oxygen atoms are coloured in red and the hydroxyl oxygen atoms of the threonine residues have been slightly enlarged. The opposing directions of the threonine side-chain in the presence and absence of the phosphoryl group are apparent. (b) A comparison of Asp55, Thr84 and Phe103 of Ca 2+ -bound N-Spo0A ~ phosphate (cyan) with the corresponding Asp57, Thr87 and Tyr106 of Mg 2+ -coordinated CheY (pink), emphasising the concerted movements upon phosphorylation. The structures were superimposed on the main-chain atoms of 112 residues with an rmsdelta of 1.5 Å .
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 294, 9-0) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21346797 V.Parashar, N.Mirouze, D.A.Dubnau, and M.B.Neiditch (2011).
Structural basis of response regulator dephosphorylation by rap phosphatases.
  PLoS Biol, 9, e1000589.
PDB code: 3q15
20164409 N.J.Baxter, M.W.Bowler, T.Alizadeh, M.J.Cliff, A.M.Hounslow, B.Wu, D.B.Berkowitz, N.H.Williams, G.M.Blackburn, and J.P.Waltho (2010).
Atomic details of near-transition state conformers for enzyme phosphoryl transfer revealed by MgF-3 rather than by phosphoranes.
  Proc Natl Acad Sci U S A, 107, 4555-4560.
PDB codes: 2wf5 2whe
20197546 Q.Ye, S.W.Crawley, Y.Yang, G.P.Côté, and Z.Jia (2010).
Crystal structure of the alpha-kinase domain of Dictyostelium myosin heavy chain kinase A.
  Sci Signal, 3, ra17.
PDB codes: 3lkm 3lla 3lmh 3lmi
20825354 T.Krell, J.Lacal, A.Busch, H.Silva-Jiménez, M.E.Guazzaroni, and J.L.Ramos (2010).
Bacterial sensor kinases: diversity in the recognition of environmental signals.
  Annu Rev Microbiol, 64, 539-559.  
19699748 J.D.Batchelor, H.J.Sterling, E.Hong, E.R.Williams, and D.E.Wemmer (2009).
Receiver domains control the active-state stoichiometry of Aquifex aeolicus sigma54 activator NtrC4, as revealed by electrospray ionization mass spectrometry.
  J Mol Biol, 393, 634-643.  
19800110 P.Casino, V.Rubio, and A.Marina (2009).
Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction.
  Cell, 139, 325-336.
PDB codes: 3dge 3dgf 3gl9
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
19581368 S.D.Seredick, B.M.Seredick, D.Baker, and G.B.Spiegelman (2009).
An A257V mutation in the bacillus subtilis response regulator Spo0A prevents regulated expression of promoters with low-consensus binding sites.
  J Bacteriol, 191, 5489-5498.  
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.  
18832306 D.Ruiz, P.Salinas, M.L.Lopez-Redondo, M.L.Cayuela, A.Marina, and A.Contreras (2008).
Phosphorylation-independent activation of the atypical response regulator NblR.
  Microbiology, 154, 3002-3015.  
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.  
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
18077416 C.Toyoshima, Y.Norimatsu, S.Iwasawa, T.Tsuda, and H.Ogawa (2007).
How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump.
  Proc Natl Acad Sci U S A, 104, 19831-19836.
PDB codes: 2zbe 2zbf 2zbg
17586650 E.A.Hussa, T.M.O'Shea, C.L.Darnell, E.G.Ruby, and K.L.Visick (2007).
Two-component response regulators of Vibrio fischeri: identification, mutagenesis, and characterization.
  J Bacteriol, 189, 5825-5838.  
17491010 E.Hong, H.M.Lee, H.Ko, D.U.Kim, B.Y.Jeon, J.Jung, J.Shin, S.A.Lee, Y.Kim, Y.H.Jeon, C.Cheong, H.S.Cho, and W.Lee (2007).
Structure of an atypical orphan response regulator protein supports a new phosphorylation-independent regulatory mechanism.
  J Biol Chem, 282, 20667-20675.
PDB codes: 2hqn 2hqo 2hqr
17511470 N.Friedland, T.R.Mack, M.Yu, L.W.Hung, T.C.Terwilliger, G.S.Waldo, and A.M.Stock (2007).
Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation.
  Biochemistry, 46, 6733-6743.
PDB code: 2gwr
17697997 P.Wassmann, C.Chan, R.Paul, A.Beck, H.Heerklotz, U.Jenal, and T.Schirmer (2007).
Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition.
  Structure, 15, 915-927.
PDB code: 2v0n
17050920 A.M.Stock, and J.Guhaniyogi (2006).
A new perspective on response regulator activation.
  J Bacteriol, 188, 7328-7330.  
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.  
16628247 E.S.Groban, A.Narayanan, and M.P.Jacobson (2006).
Conformational changes in protein loops and helices induced by post-translational phosphorylation.
  PLoS Comput Biol, 2, e32.  
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
16475196 M.S.Formaneck, L.Ma, and Q.Cui (2006).
Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).
  Proteins, 63, 846-867.  
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.  
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
16831870 S.Castang, S.Reverchon, P.Gouet, and W.Nasser (2006).
Direct evidence for the modulation of the activity of the Erwinia chrysanthemi quorum-sensing regulator ExpR by acylhomoserine lactone pheromone.
  J Biol Chem, 281, 29972-29987.  
16888621 V.Castilla-Llorente, D.Muñoz-Espín, L.Villar, M.Salas, and W.J.Meijer (2006).
Spo0A, the key transcriptional regulator for entrance into sporulation, is an inhibitor of DNA replication.
  EMBO J, 25, 3890-3899.  
16319927 A.Marina, C.D.Waldburger, and W.A.Hendrickson (2005).
Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein.
  EMBO J, 24, 4247-4259.
PDB code: 2c2a
15659154 I.Barák, E.Ricca, and S.M.Cutting (2005).
From fundamental studies of sporulation to applied spore research.
  Mol Microbiol, 55, 330-338.  
16321923 K.I.Varughese (2005).
Conformational changes of Spo0F along the phosphotransfer pathway.
  J Bacteriol, 187, 8221-8227.  
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.  
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
15452115 A.Barth, and N.Bezlyepkina (2004).
P-O bond destabilization accelerates phosphoenzyme hydrolysis of sarcoplasmic reticulum Ca2+ -ATPase.
  J Biol Chem, 279, 51888-51896.  
14762002 A.Kumar, J.A.Brannigan, and C.P.Moran (2004).
Alpha-helix E of Spo0A is required for sigmaA- but not for sigmaH-dependent promoter activation in Bacillus subtilis.
  J Bacteriol, 186, 1078-1083.  
15240481 C.Benda, C.Scheufler, N.Tandeau de Marsac, and W.Gärtner (2004).
Crystal structures of two cyanobacterial response regulators in apo- and phosphorylated form reveal a novel dimerization motif of phytochrome-associated response regulators.
  Biophys J, 87, 476-487.
PDB codes: 1k66 1k68
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
15448704 C.Toyoshima, H.Nomura, and T.Tsuda (2004).
Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues.
  Nature, 432, 361-368.
PDB codes: 1wpe 1wpg 2z9r 2zbd
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
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.  
12950927 A.Howell, S.Dubrac, K.K.Andersen, D.Noone, J.Fert, T.Msadek, and K.Devine (2003).
Genes controlled by the essential YycG/YycF two-component system of Bacillus subtilis revealed through a novel hybrid regulator approach.
  Mol Microbiol, 49, 1639-1655.  
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
12829280 J.C.Ladds, K.Muchová, D.Blaskovic, R.J.Lewis, J.A.Brannigan, A.J.Wilkinson, and I.Barák (2003).
The response regulator Spo0A from Bacillus subtilis is efficiently phosphorylated in Escherichia coli.
  FEMS Microbiol Lett, 223, 153-157.  
14563873 J.G.Smith, J.A.Latiolais, G.P.Guanga, S.Citineni, R.E.Silversmith, and R.B.Bourret (2003).
Investigation of the role of electrostatic charge in activation of the Escherichia coli response regulator CheY.
  J Bacteriol, 185, 6385-6391.  
12614149 J.H.Zhang, G.Xiao, R.P.Gunsalus, and W.L.Hubbell (2003).
Phosphorylation triggers domain separation in the DNA binding response regulator NarL.
  Biochemistry, 42, 2552-2559.  
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.  
12022879 G.S.Anand, and A.M.Stock (2002).
Kinetic basis for the stimulatory effect of phosphorylation on the methylesterase activity of CheB.
  Biochemistry, 41, 6752-6760.  
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
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.  
12381847 S.Da Re, T.Tolstykh, P.M.Wolanin, and J.B.Stock (2002).
Genetic analysis of response regulator activation in bacterial chemotaxis suggests an intermolecular mechanism.
  Protein Sci, 11, 2644-2654.  
12067336 S.J.Stephenson, and M.Perego (2002).
Interaction surface of the Spo0A response regulator with the Spo0E phosphatase.
  Mol Microbiol, 44, 1455-1467.  
12206664 S.Park, H.Zhang, A.D.Jones, and B.T.Nixon (2002).
Biochemical evidence for multiple dimeric states of the Sinorhizobium meliloti DctD receiver domain.
  Biochemistry, 41, 10934-10941.  
12453214 T.Yoshida, L.Qin, and M.Inouye (2002).
Formation of the stoichiometric complex of EnvZ, a histidine kinase, with its response regulator, OmpR.
  Mol Microbiol, 46, 1273-1282.  
11847283 Y.J.Im, S.H.Rho, C.M.Park, S.S.Yang, J.G.Kang, J.Y.Lee, P.S.Song, and S.H.Eom (2002).
Crystal structure of a cyanobacterial phytochrome response regulator.
  Protein Sci, 11, 614-624.
PDB codes: 1i3c 1jlk
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
11406410 A.H.West, and A.M.Stock (2001).
Histidine kinases and response regulator proteins in two-component signaling systems.
  Trends Biochem Sci, 26, 369-376.  
11438683 H.Cho, W.Wang, R.Kim, H.Yokota, S.Damo, S.H.Kim, D.Wemmer, S.Kustu, and D.Yan (2001).
BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF(3)(-) complex with phosphoserine phosphatase.
  Proc Natl Acad Sci U S A, 98, 8525-8530.
PDB code: 1j97
11353835 M.Schuster, R.E.Silversmith, and R.B.Bourret (2001).
Conformational coupling in the chemotaxis response regulator CheY.
  Proc Natl Acad Sci U S A, 98, 6003-6008.  
11134926 P.Gouet, N.Chinardet, M.Welch, V.Guillet, S.Cabantous, C.Birck, L.Mourey, and J.P.Samama (2001).
Further insights into the mechanism of function of the response regulator CheY from crystallographic studies of the CheY--CheA(124--257) complex.
  Acta Crystallogr D Biol Crystallogr, 57, 44-51.
PDB codes: 1ffg 1ffs 1ffw
11669626 R.L.Saxl, G.S.Anand, and A.M.Stock (2001).
Synthesis and biochemical characterization of a phosphorylated analogue of the response regulator CheB.
  Biochemistry, 40, 12896-12903.  
11342136 W.Wang, R.Kim, J.Jancarik, H.Yokota, and S.H.Kim (2001).
Crystal structure of phosphoserine phosphatase from Methanococcus jannaschii, a hyperthermophile, at 1.8 A resolution.
  Structure, 9, 65-71.
PDB code: 1f5s
11092844 A.Bren, and M.Eisenbach (2000).
How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation.
  J Bacteriol, 182, 6865-6873.  
11121774 A.L.Sonenshein (2000).
Control of sporulation initiation in Bacillus subtilis.
  Curr Opin Microbiol, 3, 561-566.  
10966457 A.M.Stock, V.L.Robinson, and P.N.Goudreau (2000).
Two-component signal transduction.
  Annu Rev Biochem, 69, 183-215.  
10754569 D.R.Buckler, G.S.Anand, and A.M.Stock (2000).
Response-regulator phosphorylation and activation: a two-way street?
  Trends Microbiol, 8, 153-156.  
10754235 F.Schmeisser, J.A.Brannigan, R.J.Lewis, A.J.Wilkinson, P.Youngman, and I.Barák (2000).
A new mutation in spo0A with intragenic suppressors in the effector domain.
  FEMS Microbiol Lett, 185, 123-128.  
10745001 J.A.Hoch (2000).
Two-component and phosphorelay signal transduction.
  Curr Opin Microbiol, 3, 165-170.  
10837243 J.Stock, and S.Da Re (2000).
Signal transduction: response regulators on and off.
  Curr Biol, 10, R420-R424.  
10997904 J.Zapf, U.Sen, Madhusudan, J.A.Hoch, and K.I.Varughese (2000).
A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction.
  Structure, 8, 851-862.
PDB code: 1f51
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 code is shown on the right.