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PDBsum entry 1dbw

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protein ligands Protein-protein interface(s) links
Transcription PDB id
1dbw
Jmol
Contents
Protein chains
123 a.a. *
Ligands
15P
Waters ×148
* Residue conservation analysis
PDB id:
1dbw
Name: Transcription
Title: Crystal structure of fixj-n
Structure: Transcriptional regulatory protein fixj. Chain: a, b. Fragment: fixj receiver domain (residues 1-126). Engineered: yes. Mutation: yes
Source: Sinorhizobium meliloti. Organism_taxid: 382. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.187     R-free:   0.224
Authors: P.Gouet,B.Fabry,V.Guillet,C.Birck,L.Mourey,D.Kahn,J.P.Samama
Key ref:
P.Gouet et al. (1999). Structural transitions in the FixJ receiver domain. Structure, 7, 1517-1526. PubMed id: 10647182 DOI: 10.1016/S0969-2126(00)88342-2
Date:
03-Nov-99     Release date:   26-Nov-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P10958  (FIXJ_RHIME) -  Transcriptional regulatory protein FixJ
Seq:
Struc:
204 a.a.
123 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 
  Biochemical function     two-component response regulator activity     1 term  

 

 
DOI no: 10.1016/S0969-2126(00)88342-2 Structure 7:1517-1526 (1999)
PubMed id: 10647182  
 
 
Structural transitions in the FixJ receiver domain.
P.Gouet, B.Fabry, V.Guillet, C.Birck, L.Mourey, D.Kahn, J.P.Samama.
 
  ABSTRACT  
 
BACKGROUND: Two-component signal transduction pathways are sophisticated phosphorelay cascades widespread in prokaryotes and also found in fungi, molds and plants. FixL/FixJ is a prototypical system responsible for the regulation of nitrogen fixation in the symbiotic bacterium Sinorhizobium meliloti. In microaerobic conditions the membrane-bound kinase FixL uses ATP to transphosphorylate a histidine residue, and the response regulator FixJ transfers the phosphoryl group from the phosphohistidine to one of its own aspartate residues in a Mg(2+)-dependent mechanism. RESULTS: Seven X-ray structures of the unphosphorylated N-terminal receiver domain of FixJ (FixJN) have been solved from two crystal forms soaked in different conditions. Three conformations of the protein were found. In the first case, the protein fold impairs metal binding in the active site and the structure reveals a receiver domain that is self-inhibited for catalysis. In the second conformation, the canonical geometry of the active site is attained, and subsequent metal binding to the protein induces minimal conformational changes. The third conformation illustrates a non-catalytic form of the protein where unwinding of the N terminus of helix alpha 1 has occurred. Interconversion of the canonical and self-inhibited conformations requires a large conformational change of the beta 3-alpha 3 loop region. CONCLUSIONS: These unphosphorylated structures of FixJN stress the importance of flexible peptide segments that delineate the active site. Their movements may act as molecular switches that define the functional status of the protein. Such observations are in line with structural and biochemical results obtained on other response regulator proteins and may illustrate general features that account for the specificity of protein-protein interactions.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Stereoview of the superposed atypical structure (mainchain atoms in green; filled sidechain bonds) and self-inhibited structure (mainchain atoms in black; open sidechain bonds).
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1517-1526) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19445950 E.S.Groban, E.J.Clarke, H.M.Salis, S.M.Miller, and C.A.Voigt (2009).
Kinetic buffering of cross talk between bacterial two-component sensors.
  J Mol Biol, 390, 380-393.  
18615432 E.Kinoshita, E.Kinoshita-Kikuta, M.Matsubara, S.Yamada, H.Nakamura, Y.Shiro, Y.Aoki, K.Okita, and T.Koike (2008).
Separation of phosphoprotein isotypes having the same number of phosphate groups using phosphate-affinity SDS-PAGE.
  Proteomics, 8, 2994-3003.  
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
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
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.  
16929106 M.Solà, D.L.Drew, A.G.Blanco, F.X.Gomis-Rüth, and M.Coll (2006).
The cofactor-induced pre-active conformation in PhoB.
  Acta Crystallogr D Biol Crystallogr, 62, 1046-1057.
PDB code: 2iyn
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.  
15772084 M.A.Seeliger, M.Spichty, S.E.Kelly, M.Bycroft, S.M.Freund, M.Karplus, and L.S.Itzhaki (2005).
Role of conformational heterogeneity in domain swapping and adapter function of the Cks proteins.
  J Biol Chem, 280, 30448-30459.  
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
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
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.  
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.  
12176390 U.Ermler, C.H.Hagemeier, A.Roth, U.Demmer, W.Grabarse, E.Warkentin, and J.A.Vorholt (2002).
Structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens AM1.
  Structure, 10, 1127-1137.
PDB codes: 1lu9 1lua
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
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
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
10837243 J.Stock, and S.Da Re (2000).
Signal transduction: response regulators on and off.
  Curr Biol, 10, R420-R424.  
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.