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PDBsum entry 1dc7

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Signaling protein PDB id
1dc7
Jmol
Contents
Protein chain
124 a.a. *
* Residue conservation analysis
PDB id:
1dc7
Name: Signaling protein
Title: Structure of a transiently phosphorylated "switch" in bacterial signal transduction
Structure: Nitrogen regulation protein. Chain: a. Fragment: n-terminal receiver domain(1-124). Synonym: ntrc. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 1 models
Authors: D.Kern,B.F.Volkman,P.Luginbuhl,M.J.Nohaile,S.Kustu, D.E.Wemmer
Key ref:
D.Kern et al. (1999). Structure of a transiently phosphorylated switch in bacterial signal transduction. Nature, 402, 894-898. PubMed id: 10622255 DOI: 10.1038/47273
Date:
04-Nov-99     Release date:   05-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P41789  (NTRC_SALTY) -  Nitrogen regulation protein NR(I)
Seq:
Struc:
469 a.a.
124 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 
  Biochemical function     two-component response regulator activity     1 term  

 

 
DOI no: 10.1038/47273 Nature 402:894-898 (1999)
PubMed id: 10622255  
 
 
Structure of a transiently phosphorylated switch in bacterial signal transduction.
D.Kern, B.F.Volkman, P.Luginbühl, M.J.Nohaile, S.Kustu, D.E.Wemmer.
 
  ABSTRACT  
 
Receiver domains are the dominant molecular switches in bacterial signalling. Although several structures of non-phosphorylated receiver domains have been reported, a detailed structural understanding of the activation arising from phosphorylation has been impeded by the very short half-lives of the aspartylphosphate linkages. Here we present the first structure of a receiver domain in its active state, the phosphorylated receiver domain of the bacterial enhancer-binding protein NtrC (nitrogen regulatory protein C). Nuclear magnetic resonance spectra were taken during steady-state autophosphorylation/dephosphorylation, and three-dimensional spectra from multiple samples were combined. Phosphorylation induces a large conformational change involving a displacement of beta-strands 4 and 5 and alpha-helices 3 and 4 away from the active site, a register shift and an axial rotation in helix 4. This creates an exposed hydrophobic surface that is likely to transmit the signal to the transcriptional activation domain.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: The structure of the phosphorylated receiver domain of NtrC. The 20 conformers with the lowest DYANA^28 target function were superimposed using the backbone atoms N, C and C' of residues 3–83 ( 1–loop 3), 87–96 ( 4) and 98–122 ( 5– 5), the best-defined areas (global backbone displacement <2.0 Å). Helices are coloured in yellow, strands in magenta and loops and chain termini in cyan. The side chain of the phosphorylated D54 is shown in green. The secondary structure elements are labelled as they are referred to in the text.
Figure 3.
Figure 3: Molecular switch upon phosphorylation of D54 in NtrC^r.
Figure 3 : Molecular switch upon phosphorylation of D54 in NtrCr. Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com-
Superimposed ribbon structures of P-NtrC^r (yellow/orange) and NtrC^r (cyan/blue), generated using the conformer closest to the mean structure for each. The molecule has been rotated by 20° about the vertical axis with respect to Fig. 2 to emphasize the regions of structural differences between the two forms. Structures were superimposed using residues 4–9, 14–53 and 108–121, which are indicated in darker colours (orange and blue). The regions of greatest difference are highlighted (yellow and cyan, the switch area) and the corresponding secondary structure elements are labelled, with the prime indicating the unphosphorylated form. Upon phosphorylation of D54, -strands 4 and 5 and -helices 3 and 4 tilt to the left—away from the active site. In addition, a register shift by about two amino-acid residues from the N to the C terminus and a rotation by about 100° about the helical axis are induced in helix 4 upon phosphorylation. The rotation results in a change in orientation of the hydrophobic side chains in helix 4 from the inside to the outside.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 402, 894-898) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21054445 V.Shingler (2011).
Signal sensory systems that impact σ⁵⁴ -dependent transcription.
  FEMS Microbiol Rev, 35, 425-440.  
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
20735776 J.Herrou, R.Foreman, A.Fiebig, and S.Crosson (2010).
A structural model of anti-anti-σ inhibition by a two-component receiver domain: the PhyR stress response regulator.
  Mol Microbiol, 78, 290-304.
PDB code: 3n0r
20385843 K.Itoh, and M.Sasai (2010).
Entropic mechanism of large fluctuation in allosteric transition.
  Proc Natl Acad Sci U S A, 107, 7775-7780.  
21153779 N.Chandra, P.Anand, and K.Yeturu (2010).
Structural bioinformatics: Deriving biological insights from protein structures.
  Interdiscip Sci, 2, 347-366.  
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.  
21058670 R.Otten, J.Villali, D.Kern, and F.A.Mulder (2010).
Probing microsecond time scale dynamics in proteins by methyl (1)H Carr-Purcell-Meiboom-Gill relaxation dispersion NMR measurements. Application to activation of the signaling protein NtrC(r).
  J Am Chem Soc, 132, 17004-17014.  
20826346 Z.Cheng, Y.W.He, S.C.Lim, R.Qamra, M.A.Walsh, L.H.Zhang, and H.Song (2010).
Structural basis of the sensor-synthase interaction in autoinduction of the quorum sensing signal DSF biosynthesis.
  Structure, 18, 1199-1209.
PDB codes: 3m6m 3m6n
20005804 A.K.Gardino, J.Villali, A.Kivenson, M.Lei, C.F.Liu, P.Steindel, E.Z.Eisenmesser, W.Labeikovsky, M.Wolf-Watz, M.W.Clarkson, and D.Kern (2009).
Transient non-native hydrogen bonds promote activation of a signaling protein.
  Cell, 139, 1109-1118.  
19299505 D.Kaiserman, A.M.Buckle, P.Van Damme, J.A.Irving, R.H.Law, A.Y.Matthews, T.Bashtannyk-Puhalovich, C.Langendorf, P.Thompson, J.Vandekerckhove, K.Gevaert, J.C.Whisstock, and P.I.Bird (2009).
Structure of granzyme C reveals an unusual mechanism of protease autoinhibition.
  Proc Natl Acad Sci U S A, 106, 5587-5592.
PDB codes: 3fzz 3g01
19466817 E.Vanden-Eijnden, and M.Venturoli (2009).
Revisiting the finite temperature string method for the calculation of reaction tubes and free energies.
  J Chem Phys, 130, 194103.  
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.  
19368477 K.Itoh, and M.Sasai (2009).
Multidimensional theory of protein folding.
  J Chem Phys, 130, 145104.  
19576227 M.Lei, J.Velos, A.Gardino, A.Kivenson, M.Karplus, and D.Kern (2009).
Segmented transition pathway of the signaling protein nitrogen regulatory protein C.
  J Mol Biol, 392, 823-836.  
19246748 R.Shrivastava, A.K.Ghosh, and A.K.Das (2009).
Intra- and intermolecular domain interactions among novel two-component system proteins coded by Rv0600c, Rv0601c and Rv0602c of Mycobacterium tuberculosis.
  Microbiology, 155, 772-779.  
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.  
19371748 T.R.Mack, R.Gao, and A.M.Stock (2009).
Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB.
  J Mol Biol, 389, 349-364.  
19246239 U.Jenal, and M.Y.Galperin (2009).
Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics.
  Curr Opin Microbiol, 12, 152-160.  
18290641 A.C.Pan, D.Sezer, and B.Roux (2008).
Finding transition pathways using the string method with swarms of trajectories.
  J Phys Chem B, 112, 3432-3440.  
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
18412261 M.S.Liu, B.D.Todd, S.Yao, Z.P.Feng, R.S.Norton, and R.J.Sadus (2008).
Coarse-grained dynamics of the receiver domain of NtrC: fluctuations, correlations and implications for allosteric cooperativity.
  Proteins, 73, 218-227.  
18662309 M.de Been, M.J.Bart, T.Abee, R.J.Siezen, and C.Francke (2008).
The identification of response regulator-specific binding sites reveals new roles of two-component systems in Bacillus cereus and closely related low-GC Gram-positives.
  Environ Microbiol, 10, 2796-2809.  
18631241 R.Gao, Y.Tao, and A.M.Stock (2008).
System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids.
  Mol Microbiol, 69, 1358-1372.  
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
17400245 C.Park, S.Zhou, J.Gilmore, and S.Marqusee (2007).
Energetics-based protein profiling on a proteomic scale: identification of proteins resistant to proteolysis.
  J Mol Biol, 368, 1426-1437.  
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
17433693 R.Gao, T.R.Mack, and A.M.Stock (2007).
Bacterial response regulators: versatile regulatory strategies from common domains.
  Trends Biochem Sci, 32, 225-234.  
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
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
16740923 M.Y.Galperin (2006).
Structural classification of bacterial response regulators: diversity of output domains and domain combinations.
  J Bacteriol, 188, 4169-4182.  
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.  
16751184 S.De Carlo, B.Chen, T.R.Hoover, E.Kondrashkina, E.Nogales, and B.T.Nixon (2006).
The structural basis for regulated assembly and function of the transcriptional activator NtrC.
  Genes Dev, 20, 1485-1495.  
16321925 D.E.Wemmer, and D.Kern (2005).
Beryllofluoride binding mimics phosphorylation of aspartate in response regulators.
  J Bacteriol, 187, 8229-8230.  
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.  
16154086 M.Milani, L.Leoni, G.Rampioni, E.Zennaro, P.Ascenzi, and M.Bolognesi (2005).
An active-like structure in the unphosphorylated StyR response regulator suggests a phosphorylation- dependent allosteric activation mechanism.
  Structure, 13, 1289-1297.
PDB codes: 1yio 1zn2
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
14563853 A.C.Harrod, X.Yang, M.Junker, and L.Reitzer (2004).
Evidence for a second interaction between the regulatory amino-terminal and central output domains of the response regulator NtrC (nitrogen regulator I) in Escherichia coli.
  J Biol Chem, 279, 2350-2359.  
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.  
14739317 M.M.Teeter (2004).
Myoglobin cavities provide interior ligand pathway.
  Protein Sci, 13, 313-318.  
15208307 X.F.Yang, Y.Ji, B.L.Schneider, and L.Reitzer (2004).
Phosphorylation-independent dimer-dimer interactions by the enhancer-binding activator NtrC of Escherichia coli: a third function for the C-terminal domain.
  J Biol Chem, 279, 36708-36714.  
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.  
12925804 L.Sallai, J.Hendle, and P.A.Tucker (2003).
X-ray crystallographic characterization and phasing of an NtrC homologue.
  Acta Crystallogr D Biol Crystallogr, 59, 1656-1658.  
14568156 M.H.Rashid, C.Rajanna, A.Ali, and D.K.Karaolis (2003).
Identification of genes involved in the switch between the smooth and rugose phenotypes of Vibrio cholerae.
  FEMS Microbiol Lett, 227, 113-119.  
14561776 S.Y.Lee, A.De La Torre, D.Yan, S.Kustu, B.T.Nixon, and D.E.Wemmer (2003).
Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains.
  Genes Dev, 17, 2552-2563.
PDB codes: 1ny5 1ny6
14503005 T.Kakimoto (2003).
Perception and signal transduction of cytokinins.
  Annu Rev Plant Biol, 54, 605-627.  
12455952 A.D.Ault, J.S.Fassler, and R.J.Deschenes (2002).
Altered phosphotransfer in an activated mutant of the Saccharomyces cerevisiae two-component osmosensor Sln1p.
  Eukaryot Cell, 1, 174-180.  
11966823 D.Devos, J.Garmendia, V.de Lorenzo, and A.Valencia (2002).
Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: a structural model of its N-terminal domain.
  Environ Microbiol, 4, 29-41.  
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.  
11741861 I.Martínez-Argudo, P.Salinas, R.Maldonado, and A.Contreras (2002).
Domain interactions on the ntr signal transduction pathway: two-hybrid analysis of mutant and truncated derivatives of histidine kinase NtrB.
  J Bacteriol, 184, 200-206.  
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.  
12438647 S.B.Williams, I.Vakonakis, S.S.Golden, and A.C.LiWang (2002).
Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism.
  Proc Natl Acad Sci U S A, 99, 15357-15362.
PDB codes: 1m2e 1m2f
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.  
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.  
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.  
11264542 B.F.Volkman, D.Lipson, D.E.Wemmer, and D.Kern (2001).
Two-state allosteric behavior in a single-domain signaling protein.
  Science, 291, 2429-2433.  
11442836 E.Klauck, M.Lingnau, and R.Hengge-Aronis (2001).
Role of the response regulator RssB in sigma recognition and initiation of sigma proteolysis in Escherichia coli.
  Mol Microbiol, 40, 1381-1390.  
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
11282468 H.Xu, and T.R.Hoover (2001).
Transcriptional regulation at a distance in bacteria.
  Curr Opin Microbiol, 4, 138-144.  
11269305 M.Buck, and M.K.Rosen (2001).
Structural biology. Flipping a switch.
  Science, 291, 2329-2330.  
11244058 M.P.Allen, K.B.Zumbrennen, and W.R.McCleary (2001).
Genetic evidence that the alpha5 helix of the receiver domain of PhoB is involved in interdomain interactions.
  J Bacteriol, 183, 2204-2211.  
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
11459948 P.R.Thompson, and P.A.Cole (2001).
Probing the mechanism of enzymatic phosphoryl transfer with a chemical trick.
  Proc Natl Acad Sci U S A, 98, 8170-8171.  
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.  
11238986 T.Arcondéguy, R.Jack, and M.Merrick (2001).
P(II) signal transduction proteins, pivotal players in microbial nitrogen control.
  Microbiol Mol Biol Rev, 65, 80.  
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.  
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
  10850799 G.S.Anand, P.N.Goudreau, J.K.Lewis, and A.M.Stoc (2000).
Evidence for phosphorylation-dependent conformational changes in methylesterase CheB.
  Protein Sci, 9, 898-906.  
11114513 I.Schlichting, and K.Chu (2000).
Trapping intermediates in the crystal: ligand binding to myoglobin.
  Curr Opin Struct Biol, 10, 744-752.  
10960104 J.Lee, J.T.Owens, I.Hwang, C.Meares, and S.Kustu (2000).
Phosphorylation-induced signal propagation in the response regulator ntrC.
  J Bacteriol, 182, 5188-5195.  
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
10894718 M.Buck, M.T.Gallegos, D.J.Studholme, Y.Guo, and J.D.Gralla (2000).
The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor.
  J Bacteriol, 182, 4129-4136.  
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.