PDBsum entry 1krw

Go to PDB code: 
protein links
Signaling protein PDB id
Protein chain
124 a.a. *
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Solution structure and backbone dynamics of beryllofluoride- activated ntrc receiver domain
Structure: Nitrogen regulation protein nr(i). Chain: a. Fragment: n-terminal domain: receiver domain, residues 1- 124. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli. Expression_system_taxid: 511693.
NMR struc: 26 models
Authors: C.A.Hastings,S.-Y.Lee,H.S.Cho,D.Yan,S.Kustu,D.E.Wemmer
Key ref:
C.A.Hastings et al. (2003). High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain. Biochemistry, 42, 9081-9090. PubMed id: 12885241 DOI: 10.1021/bi0273866
10-Jan-02     Release date:   19-Aug-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P41789  (NTRC_SALTY) -  Nitrogen regulation protein NR(I)
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: 10.1021/bi0273866 Biochemistry 42:9081-9090 (2003)
PubMed id: 12885241  
High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain.
C.A.Hastings, S.Y.Lee, H.S.Cho, D.Yan, S.Kustu, D.E.Wemmer.
Bacterial receiver domains mediate the cellular response to environmental changes through conformational changes induced by phosphorylation of a conserved aspartate residue. While the structures of several activated receiver domains have recently been determined, there is substantial variation in the conformational changes occurring upon activation. Here we present the high-resolution structure of the activated NtrC receiver domain (BeF(3)(-)-NtrC(r) complex) determined using NMR data, including residual dipolar couplings, yielding a family of structures with a backbone rmsd of 0.57 +/- 0.08 A, which is compared with the previous lower-resolution structure of the phosphorylated protein. Both phosphorylation and beryllofluoride addition induce a shift in register and an axial rotation of alpha-helix 4. In this high-resolution structure, we are able to observe a concerted change in the positions of Thr82 and Tyr101; this correlated change in two conserved residues (termed Y-T coupling) has been considered a general feature of the conformational change in receiver domains upon activation. In NtrC, this correlated side chain shift, leading to the helix reorientation, is distinctly different from the smaller reorganization seen in other activated receiver domains, and involves numerous other residues which do not participate in conformational changes seen in the other systems. Titration of the activated receiver domain with peptides from the NtrC ATPase domain provides direct evidence for interactions on the rearranged face of the receiver domain, which are likely to be responsible for enabling assembly into the active aggregate. Analysis of the active structure also suggests that His84 may play a role in controlling the phosphate hydrolysis rate.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20966074 Z.H.Chen, C.Schilde, and P.Schaap (2010).
Functional dissection of adenylate cyclase R, an inducer of spore encapsulation.
  J Biol Chem, 285, 41724-41731.  
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.  
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.  
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
18208392 B.Chen, T.A.Sysoeva, S.Chowdhury, and B.T.Nixon (2008).
Regulation and action of the bacterial enhancer-binding protein AAA+ domains.
  Biochem Soc Trans, 36, 89-93.  
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.  
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.  
17617222 G.Bogel, H.Schrempf, and D.Ortiz de Orué Lucana (2007).
DNA-binding characteristics of the regulator SenR in response to phosphorylation by the sensor histidine autokinase SenS from Streptomyces reticuli.
  FEBS J, 274, 3900-3913.  
17157497 M.Rappas, D.Bose, and X.Zhang (2007).
Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription.
  Curr Opin Struct Biol, 17, 110-116.  
17640875 R.Paul, S.Abel, P.Wassmann, A.Beck, H.Heerklotz, and U.Jenal (2007).
Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization.
  J Biol Chem, 282, 29170-29177.  
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
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.  
16321924 D.E.Wemmer, and D.Kern (2005).
Rebuttal: conformational changes of Spo0F along the phosphotransfer pathway.
  J Bacteriol, 187, 8228.  
16321925 D.E.Wemmer, and D.Kern (2005).
Beryllofluoride binding mimics phosphorylation of aspartate in response regulators.
  J Bacteriol, 187, 8229-8230.  
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.  
15317778 A.A.Pioszak, and A.J.Ninfa (2004).
Mutations altering the N-terminal receiver domain of NRI (NtrC) That prevent dephosphorylation by the NRII-PII complex in Escherichia coli.
  J Bacteriol, 186, 5730-5740.  
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.  
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.  
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.