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Transferase PDB id
1b3q
Jmol
Contents
Protein chains
368 a.a. *
Metals
_HG ×2
Waters ×187
* Residue conservation analysis
PDB id:
1b3q
Name: Transferase
Title: Crystal structure of chea-289, a signal transducing histidin
Structure: Protein (chemotaxis protein chea). Chain: a, b. Fragment: dimerization domain, kinase domain and regulatory engineered: yes. Mutation: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Cellular_location: cytoplasm. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.213     R-free:   0.285
Authors: A.M.Bilwes,L.A.Alex,B.R.Crane,M.I.Simon
Key ref:
A.M.Bilwes et al. (1999). Structure of CheA, a signal-transducing histidine kinase. Cell, 96, 131-141. PubMed id: 9989504 DOI: 10.1016/S0092-8674(00)80966-6
Date:
14-Dec-98     Release date:   15-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q56310  (CHEA_THEMA) -  Chemotaxis protein CheA
Seq:
Struc: 		 
Seq:
Struc: 		671 a.a.
368 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.13.3  - Histidine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP
 + protein L-histidine
 = ADP
 + protein N-phospho-L-histidine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     signal transduction   5 terms 
  Biochemical function     signal transducer activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(00)80966-6 Cell 96:131-141 (1999)
PubMed id: 9989504  
 
 
Structure of CheA, a signal-transducing histidine kinase.
A.M.Bilwes, L.A.Alex, B.R.Crane, M.I.Simon.
 
  ABSTRACT  
 
Histidine kinases allow bacteria, plants, and fungi to sense and respond to their environment. The 2.6 A resolution crystal structure of Thermotoga maritima CheA (290-671) histidine kinase reveals a dimer where the functions of dimerization, ATP binding, and regulation are segregated into domains. The kinase domain is unlike Ser/Thr/Tyr kinases but resembles two ATPases, Gyrase B and Hsp90. Structural analogies within this superfamily suggest that the P1 domain of CheA provides the nucleophilic histidine and activating glutamate for phosphotransfer. The regulatory domain, which binds the homologous receptor-coupling protein CheW, topologically resembles two SH3 domains and provides different protein recognition surfaces at each end. The dimerization domain forms a central four-helix bundle about which the kinase and regulatory domains pivot on conserved hinges to modulate transphosphorylation. Different subunit conformations suggest that relative domain motions link receptor response to kinase activity.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Two Classes of Histidine KinasesGeneralized schematic diagram dividing histidine kinases into two classes based on the position in the sequence of the substrate histidine (H box) with respect to the kinase domain. H, N, G1, F, and G2 boxes are conserved sequence motifs among histidine kinases ([1]). Arrows represent the flow of phosphate through these systems. CheW is the coupling protein that interacts (hashed lines) with the sensor (receptor) and CheA. 		Figure 8.
Figure 8. Mobility about Hinges Indicated by Different Subunit ConformationsThe two subunits that form the dimer (dark colors for MOL1, light for MOL2) in the asymmetric unit are not superimposable. The positioning of MOL1 onto MOL2 was generated after least-square superposition of the C α from the dimerization domain only. Different positioning of each domain with respect to its neighbors in the asymmetric unit results from rotation around the conserved hinges (yellow) at residues 354 and 540. As a result, interfaces between domains differ in the two subunits. In the more closed conformation (light, MOL2)α 10 from the regulatory domain interacts with the kinase domain near the proposed position of the γ-phosphate (center), possibly interfering with the association of the CheA domain P1.
 
  The above figures are reprinted by permission from Cell Press: Cell (1999, 96, 131-141) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Structure of the ternary complex formed by a chemotaxis receptor signaling domain, the CheA histidine kinase, and the coupling protein CheW as determined by pulsed dipolar ESR spectroscopy.
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20117042 R.C.Stewart (2010).
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The core signaling proteins of bacterial chemotaxis assemble to form an ultrastable complex.
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19505148 A.K.Eaton, and R.C.Stewart (2009).
The two active sites of Thermotoga maritima CheA dimers bind ATP with dramatically different affinities.
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19149470 A.M.Pollard, A.M.Bilwes, and B.R.Crane (2009).
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PDB codes: 3a0r 3a0s 3a0t 3a0u 3a0v 3a0w 3a0x 3a0y 3a0z 3a10
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16740938 J.Zhao, and J.S.Parkinson (2006).
Cysteine-scanning analysis of the chemoreceptor-coupling domain of the Escherichia coli chemotaxis signaling kinase CheA.
  J Bacteriol, 188, 4321-4330.  
16369945 M.D.Baker, P.M.Wolanin, and J.B.Stock (2006).
Signal transduction in bacterial chemotaxis.
  Bioessays, 28, 9.  
16760311 M.K.Ashby, and J.Houmard (2006).
Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution.
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Structural classification of bacterial response regulators: diversity of output domains and domain combinations.
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Self-assembly of receptor/signaling complexes in bacterial chemotaxis.
  Proc Natl Acad Sci U S A, 103, 14313-14318.  
16738603 R.M.Weis (2006).
Inch by inch, row by row.
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  Antioxid Redox Signal, 8, 781-795.  
16702547 S.R.Thompson, G.H.Wadhams, and J.P.Armitage (2006).
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Reconstruction of the chemotaxis receptor-kinase assembly.
  Nat Struct Mol Biol, 13, 400-407.
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  Bioinformatics, 22, 40-49.  
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  Acta Biochim Biophys Sin (Shanghai), 38, 79-88.  
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Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein.
  EMBO J, 24, 4247-4259.
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Insights into the organization and dynamics of bacterial chemoreceptor clusters through in vivo crosslinking studies.
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Structural and chemical requirements for histidine phosphorylation by the chemotaxis kinase CheA.
  J Biol Chem, 280, 30581-30585.  
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.  
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15770502 Z.Yang, and Z.Li (2005).
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VirA of Agrobacterium tumefaciens is an intradimer transphosphorylase and can actively block vir gene expression in the absence of phenolic signals.
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The HWE histidine kinases, a new family of bacterial two-component sensor kinases with potentially diverse roles in environmental signaling.
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Making sense of it all: bacterial chemotaxis.
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Diversity in chemotaxis mechanisms among the bacteria and archaea.
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Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases.
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PDB code: 1pv0
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Dicarboxylate transport by rhizobia.
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PDB code: 1u0s
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Different evolutionary constraints on chemotaxis proteins CheW and CheY revealed by heterologous expression studies and protein sequence analysis.
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Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea.
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PDB code: 1p92
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Molecular evolution of sensory domains in cyanobacterial chemoreceptors.
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Cysteine-scanning analysis of the dimerization domain of EnvZ, an osmosensing histidine kinase.
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Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry.
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PDB codes: 1or4 1or6
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Crystal structure of the Bacillus stearothermophilus anti-sigma factor SpoIIAB with the sporulation sigma factor sigmaF.
  Cell, 108, 795-807.
PDB code: 1l0o
11799399 I.J.Griswold, H.Zhou, M.Matison, R.V.Swanson, L.P.McIntosh, M.I.Simon, and F.W.Dahlquist (2002).
The solution structure and interactions of CheW from Thermotoga maritima.
  Nat Struct Biol, 9, 121-125.
PDB code: 1k0s
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.  
12189132 J.L.Chuang, R.M.Wynn, and D.T.Chuang (2002).
The C-terminal hinge region of lipoic acid-bearing domain of E2b is essential for domain interaction with branched-chain alpha-keto acid dehydrogenase kinase.
  J Biol Chem, 277, 36905-36908.  
12270823 K.Bellenger, X.Ma, W.Shi, and Z.Yang (2002).
A CheW homologue is required for Myxococcus xanthus fruiting body development, social gliding motility, and fibril biogenesis.
  J Bacteriol, 184, 5654-5660.  
  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.  
11964403 M.Boukhvalova, R.VanBruggen, and R.C.Stewart (2002).
CheA kinase and chemoreceptor interaction surfaces on CheW.
  J Biol Chem, 277, 23596-23603.  
12119289 M.N.Levit, T.W.Grebe, and J.B.Stock (2002).
Organization of the receptor-kinase signaling array that regulates Escherichia coli chemotaxis.
  J Biol Chem, 277, 36748-36754.  
12119290 N.R.Francis, M.N.Levit, T.R.Shaikh, L.A.Melanson, J.B.Stock, and D.J.DeRosier (2002).
Subunit organization in a soluble complex of tar, CheW, and CheA by electron microscopy.
  J Biol Chem, 277, 36755-36759.  
  12372152 P.M.Wolanin, P.A.Thomason, and J.B.Stock (2002).
Histidine protein kinases: key signal transducers outside the animal kingdom.
  Genome Biol, 3, REVIEWS3013.  
11741839 R.B.Bourret, N.W.Charon, A.M.Stock, and A.H.West (2002).
Bright lights, abundant operons--fluorescence and genomic technologies advance studies of bacterial locomotion and signal transduction: review of the BLAST meeting, Cuernavaca, Mexico, 14 to 19 January 2001.
  J Bacteriol, 184, 1.  
11856347 S.Klumpp, and J.Krieglstein (2002).
Phosphorylation and dephosphorylation of histidine residues in proteins.
  Eur J Biochem, 269, 1067-1071.  
11985722 W.Tao, C.L.Malone, A.D.Ault, R.J.Deschenes, and J.S.Fassler (2002).
A cytoplasmic coiled-coil domain is required for histidine kinase activity of the yeast osmosensor, SLN1.
  Mol Microbiol, 43, 459-473.  
11574484 A.Guarné, M.S.Junop, and W.Yang (2001).
Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase.
  EMBO J, 20, 5521-5531.
PDB codes: 1ea6 1h7s 1h7u
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.  
11278487 A.Tuganova, M.D.Yoder, and K.M.Popov (2001).
An essential role of Glu-243 and His-239 in the phosphotransfer reaction catalyzed by pyruvate dehydrogenase kinase.
  J Biol Chem, 276, 17994-17999.  
11483605 C.N.Steussy, K.M.Popov, M.M.Bowker-Kinley, R.B.Sloan, R.A.Harris, and J.A.Hamilton (2001).
Structure of pyruvate dehydrogenase kinase. Novel folding pattern for a serine protein kinase.
  J Biol Chem, 276, 37443-37450.
PDB code: 1jm6
  11270409 C.P.Selitrennikoff, L.Alex, T.K.Miller, K.V.Clemons, M.I.Simon, and D.A.Stevens (2001).
COS-l, a putative two-component histidine kinase of Candida albicans, is an in vivo virulence factor.
  Med Mycol, 39, 69-74.  
11404477 D.Bhaya, A.Takahashi, and A.R.Grossman (2001).
Light regulation of type IV pilus-dependent motility by chemosensor-like elements in Synechocystis PCC6803.
  Proc Natl Acad Sci U S A, 98, 7540-7545.  
11553614 E.Karatan, M.M.Saulmon, M.W.Bunn, and G.W.Ordal (2001).
Phosphorylation of the response regulator CheV is required for adaptation to attractants during Bacillus subtilis chemotaxis.
  J Biol Chem, 276, 43618-43626.  
11298284 I.Martínez-Argudo, J.Martín-Nieto, P.Salinas, R.Maldonado, M.Drummond, and A.Contreras (2001).
Two-hybrid analysis of domain interactions involving NtrB and NtrC two-component regulators.
  Mol Microbiol, 40, 169-178.  
11172710 J.A.Carrodeguas, K.Theis, D.F.Bogenhagen, and C.Kisker (2001).
Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer.
  Mol Cell, 7, 43-54.
PDB codes: 1g5h 1g5i
11489844 J.A.Hoch, and K.I.Varughese (2001).
Keeping signals straight in phosphorelay signal transduction.
  J Bacteriol, 183, 4941-4949.  
11722727 J.R.Kirby, C.J.Kristich, M.M.Saulmon, M.A.Zimmer, L.F.Garrity, I.B.Zhulin, and G.W.Ordal (2001).
CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis.
  Mol Microbiol, 42, 573-585.  
11325944 J.S.Wright, and R.J.Kadner (2001).
The phosphoryl transfer domain of UhpB interacts with the response regulator UhpA.
  J Bacteriol, 183, 3149-3159.  
11473354 K.Richter, and J.Buchner (2001).
Hsp90: chaperoning signal transduction.
  J Cell Physiol, 188, 281-290.  
11562470 M.Machius, J.L.Chuang, R.M.Wynn, D.R.Tomchick, and D.T.Chuang (2001).
Structure of rat BCKD kinase: nucleotide-induced domain communication in a mitochondrial protein kinase.
  Proc Natl Acad Sci U S A, 98, 11218-11223.
PDB codes: 1gjv 1gkx 1gkz
11160113 M.Montagne, A.Martel, and H.Le Moual (2001).
Characterization of the catalytic activities of the PhoQ histidine protein kinase of Salmonella enterica serovar Typhimurium.
  J Bacteriol, 183, 1787-1791.  
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
11553774 S.D.Catz, J.L.Johnson, and B.M.Babior (2001).
Characterization of the nucleotide-binding capacity and the ATPase activity of the PIP3-binding protein JFC1.
  Proc Natl Acad Sci U S A, 98, 11230-11235.  
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.  
10966457 A.M.Stock, V.L.Robinson, and P.N.Goudreau (2000).
Two-component signal transduction.
  Annu Rev Biochem, 69, 183-215.  
  11121759 A.Rodrigue, Y.Quentin, A.Lazdunski, V.Méjean, and M.Foglino (2000).
Two-component systems in Pseudomonas aeruginosa: why so many?
  Trends Microbiol, 8, 498-504.  
10603474 C.J.Bakal, and J.E.Davies (2000).
No longer an exclusive club: eukaryotic signalling domains in bacteria.
  Trends Cell Biol, 10, 32-38.  
10944121 C.Prodromou, B.Panaretou, S.Chohan, G.Siligardi, R.O'Brien, J.E.Ladbury, S.M.Roe, P.W.Piper, and L.H.Pearl (2000).
The ATPase cycle of Hsp90 drives a molecular 'clamp' via transient dimerization of the N-terminal domains.
  EMBO J, 19, 4383-4392.  
10692367 D.J.Studholme, S.R.Wigneshwereraraj, M.T.Gallegos, and M.Buck (2000).
Functionality of purified sigma(N) (sigma(54)) and a NifA-like protein from the hyperthermophile Aquifex aeolicus.
  J Bacteriol, 182, 1616-1623.  
10632881 D.S.Shah, S.L.Porter, D.C.Harris, G.H.Wadhams, P.A.Hamblin, and J.P.Armitage (2000).
Identification of a fourth cheY gene in Rhodobacter sphaeroides and interspecies interaction within the bacterial chemotaxis signal transduction pathway.
  Mol Microbiol, 35, 101-112.  
10924144 J.A.Bornhorst, and J.J.Falke (2000).
Attractant regulation of the aspartate receptor-kinase complex: limited cooperative interactions between receptors and effects of the receptor modification state.
  Biochemistry, 39, 9486-9493.  
  10745001 J.A.Hoch (2000).
Two-component and phosphorelay signal transduction.
  Curr Opin Microbiol, 3, 165-170.  
11060043 J.C.Young, and F.U.Hartl (2000).
Polypeptide release by Hsp90 involves ATP hydrolysis and is enhanced by the co-chaperone p23.
  EMBO J, 19, 5930-5940.  
10981636 J.J.Falke, and S.H.Kim (2000).
Structure of a conserved receptor domain that regulates kinase activity: the cytoplasmic domain of bacterial taxis receptors.
  Curr Opin Struct Biol, 10, 462-469.  
10760172 J.M.Boyd (2000).
Localization of the histidine kinase PilS to the poles of Pseudomonas aeruginosa and identification of a localization domain.
  Mol Microbiol, 36, 153-162.  
10648522 J.M.Skidmore, D.D.Ellefson, B.P.McNamara, M.M.Couto, A.J.Wolfe, and J.R.Maddock (2000).
Polar clustering of the chemoreceptor complex in Escherichia coli occurs in the absence of complete CheA function.
  J Bacteriol, 182, 967-973.  
10660286 J.Stock, and M.Levit (2000).
Signal transduction: hair brains in bacterial chemotaxis.
  Curr Biol, 10, R11-R14.  
11015200 K.S.Pavur, A.N.Petrov, and A.G.Ryazanov (2000).
Mapping the functional domains of elongation factor-2 kinase.
  Biochemistry, 39, 12216-12224.  
10679459 L.H.Pearl, and C.Prodromou (2000).
Structure and in vivo function of Hsp90.
  Curr Opin Struct Biol, 10, 46-51.  
10869441 L.Krall, and J.W.Reed (2000).
The histidine kinase-related domain participates in phytochrome B function but is dispensable.
  Proc Natl Acad Sci U S A, 97, 8169-8174.  
10760160 L.Qin, R.Dutta, H.Kurokawa, M.Ikura, and M.Inouye (2000).
A monomeric histidine kinase derived from EnvZ, an Escherichia coli osmosensor.
  Mol Microbiol, 36, 24-32.  
11052668 R.C.Stewart, K.Jahreis, and J.S.Parkinson (2000).
Rapid phosphotransfer to CheY from a CheA protein lacking the CheY-binding domain.
  Biochemistry, 39, 13157-13165.  
10692349 S.I.Aizawa, C.S.Harwood, and R.J.Kadner (2000).
Signaling components in bacterial locomotion and sensory reception.
  J Bacteriol, 182, 1459-1471.  
11111026 T.V.Sergeyenko, and D.A.Los (2000).
Identification of secreted proteins of the cyanobacterium Synechocystis sp. strain PCC 6803.
  FEMS Microbiol Lett, 193, 213-216.  
10972797 V.Sourjik, and H.C.Berg (2000).
Localization of components of the chemotaxis machinery of Escherichia coli using fluorescent protein fusions.
  Mol Microbiol, 37, 740-751.  
10884412 Y.Zhu, L.Qin, T.Yoshida, and M.Inouye (2000).
Phosphatase activity of histidine kinase EnvZ without kinase catalytic domain.
  Proc Natl Acad Sci U S A, 97, 7808-7813.  
10199405 C.Ban, M.Junop, and W.Yang (1999).
Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair.
  Cell, 97, 85-97.
PDB codes: 1b62 1b63
10339418 J.Stock (1999).
Signal transduction: Gyrating protein kinases.
  Curr Biol, 9, R364-R367.  
10418137 L.Aravind, and C.P.Ponting (1999).
The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins.
  FEMS Microbiol Lett, 176, 111-116.  
  10647182 P.Gouet, B.Fabry, V.Guillet, C.Birck, L.Mourey, D.Kahn, and J.P.Samama (1999).
Structural transitions in the FixJ receiver domain.
  Structure, 7, 1517-1526.
PDB codes: 1dbw 1dck 1dcm
10564504 R.Dutta, L.Qin, and M.Inouye (1999).
Histidine kinases: diversity of domain organization.
  Mol Microbiol, 34, 633-640.  
10447894 S.Kaspar, R.Perozzo, S.Reinelt, M.Meyer, K.Pfister, L.Scapozza, and M.Bott (1999).
The periplasmic domain of the histidine autokinase CitA functions as a highly specific citrate receptor.
  Mol Microbiol, 33, 858-872.  
  10368305 V.L.Robinson, and A.M.Stock (1999).
High energy exchange: proteins that make or break phosphoramidate bonds.
  Structure, 7, R47-R53.  
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