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PDBsum entry 1vls

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protein links
Chemotaxis PDB id
1vls
Jmol
Contents
Protein chain
146 a.a. *
Waters ×219
* Residue conservation analysis
PDB id:
1vls
Name: Chemotaxis
Title: Ligand binding domain of the wild-type aspartate receptor
Structure: Aspartate receptor. Chain: a. Synonym: tar. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602
Biol. unit: Dimer (from PDB file)
Resolution:
1.85Å     R-factor:   0.197    
Authors: S.-H.Kim,J.I.Yeh,H.-P.Biemann,G.Prive,J.Pandit,D.E.Koshland Junior
Key ref:
J.I.Yeh et al. (1996). High-resolution structures of the ligand binding domain of the wild-type bacterial aspartate receptor. J Mol Biol, 262, 186-201. PubMed id: 8831788 DOI: 10.1006/jmbi.1996.0507
Date:
17-Sep-96     Release date:   21-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02941  (MCP2_SALTY) -  Methyl-accepting chemotaxis protein II
Seq:
Struc:
 
Seq:
Struc:
553 a.a.
146 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!
  Cellular component     membrane   1 term 
  Biological process     signal transduction   2 terms 
  Biochemical function     transmembrane signaling receptor activity     1 term  

 

 
DOI no: 10.1006/jmbi.1996.0507 J Mol Biol 262:186-201 (1996)
PubMed id: 8831788  
 
 
High-resolution structures of the ligand binding domain of the wild-type bacterial aspartate receptor.
J.I.Yeh, H.P.Biemann, G.G.Privé, J.Pandit, D.E.Koshland, S.H.Kim.
 
  ABSTRACT  
 
The high-resolution structures of the wild-type periplasmic domain of the bacterial aspartate receptor have been determined in the absence and presence of bound aspartate to 1.85 and 2.2 A resolution, respectively. As we reported earlier, in the refined structure of the complexed form of the crosslinked cysteine mutant receptor, the binding of the aspartate at the first site was mediated through four bridging water molecules while the second site showed an occupant electron density that best fit a sulfate group, which was present in the crystallization solution at high concentration. In the wild-type periplasmic domain structure two aspartate residues are bound per dimer, but with different occupancies. There exists a "strong" aspartate-binding site whose binding is again mediated by four water molecules while the second site contains aspartate whose B-factor is about 10% higher, signifying weaker binding. The interaction between the second, "weaker" aspartate with the three ligand-binding arginine side-chains is slightly different from the first site. The major difference is that there are three water molecules mediating the binding of aspartate at the second site, whereas in the first site there are four bridging water molecules. The fact that aspartate-complexed crystals of the wild-type were grown with a large excess aspartate while the cross-linked crystals were grown with equal molar aspartate may explain the difference in the stoichiometry observed. The conservation of the four bridging water molecules in the strong aspartate site of both the cross-linked and wild-type periplasmic domain may reflect an important binding motif. The periplasmic domain in the apo form is a symmetrical dimer, in which each of the subunits is equivalent, and the two aspartate binding sites are identical. Upon the binding of aspartate, the subunits are no longer symmetrical. The main difference between the aspartate-bound and unbound forms is in a small, rigid-body rotation between the subunits within a dimer. The rotation is similar in both direction and magnitude in the crosslinked and wild-type periplasmic domains. The presence of the second aspartate in the wild-type structure does not make any additional rotation compared to the single-site binding. The conservation of the small angular change in vitro suggests that the inter-subunit rotation may have relevance to the understanding of the mechanism of transmembrane signal transduction in vivo.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Electron densities of ligand-binding sites calculated in omit Fo - Fc map and contoured at the 3s level. (a) The major ligand binding site (site I) of WT protein. (b) The major site for crosslinked protein. (c) The minor site (site I') for the WT protein. (d) The minor site for crosslinked minor site. SA: simulated annealing.
Figure 6.
Figure 6. (a) After subunit A of WT apo protein is superimposed to the A subunit of WT complex, while carrying over the B subunits, each of the distances of the corresponding a-carbon residues are calculated and indicated. Helical regions are indicated on top. (b) The same as (a) except that B subunits are superimposed first while carrying over the A subunits. (c) and (d) are equivalent to (a) and (b), respectively, for the crosslinked protein.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 262, 186-201) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21360620 J.Lacal, C.García-Fontana, C.Callejo-García, J.L.Ramos, and T.Krell (2011).
Physiologically relevant divalent cations modulate citrate recognition by the McpS chemoreceptor.
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  21087385 T.Krell, J.Lacal, F.Muñoz-Martínez, J.A.Reyes-Darias, B.H.Cadirci, C.García-Fontana, and J.L.Ramos (2011).
Diversity at its best: bacterial taxis.
  Environ Microbiol, 13, 1115-1124.  
20199597 C.G.Earnhart, D.V.Leblanc, K.E.Alix, D.C.Desrosiers, J.D.Radolf, and R.T.Marconi (2010).
Identification of residues within ligand-binding domain 1 (LBD1) of the Borrelia burgdorferi OspC protein required for function in the mammalian environment.
  Mol Microbiol, 76, 393-408.  
19864420 G.D.Glekas, R.M.Foster, J.R.Cates, J.A.Estrella, M.J.Wawrzyniak, C.V.Rao, and G.W.Ordal (2010).
A PAS domain binds asparagine in the chemotaxis receptor McpB in Bacillus subtilis.
  J Biol Chem, 285, 1870-1878.  
19785456 I.Bahar, T.R.Lezon, A.Bakan, and I.H.Shrivastava (2010).
Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.
  Chem Rev, 110, 1463-1497.  
20223701 J.Cheung, and W.A.Hendrickson (2010).
Sensor domains of two-component regulatory systems.
  Curr Opin Microbiol, 13, 116-123.  
20738376 J.Lacal, C.García-Fontana, F.Muñoz-Martínez, J.L.Ramos, and T.Krell (2010).
Sensing of environmental signals: classification of chemoreceptors according to the size of their ligand binding regions.
  Environ Microbiol, 12, 2873-2884.  
20204450 S.J.Facey, and A.Kuhn (2010).
Biogenesis of bacterial inner-membrane proteins.
  Cell Mol Life Sci, 67, 2343-2362.  
20212168 W.L.Ng, Y.Wei, L.J.Perez, J.Cong, T.Long, M.Koch, M.F.Semmelhack, N.S.Wingreen, and B.L.Bassler (2010).
Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules.
  Proc Natl Acad Sci U S A, 107, 5575-5580.  
19149470 A.M.Pollard, A.M.Bilwes, and B.R.Crane (2009).
The structure of a soluble chemoreceptor suggests a mechanism for propagating conformational signals.
  Biochemistry, 48, 1936-1944.
PDB codes: 3g67 3g6b
19217390 J.Cheung, and W.A.Hendrickson (2009).
Structural analysis of ligand stimulation of the histidine kinase NarX.
  Structure, 17, 190-201.
PDB codes: 3ezh 3ezi
18940922 C.M.Khursigara, X.Wu, P.Zhang, J.Lefman, and S.Subramaniam (2008).
Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors.
  Proc Natl Acad Sci U S A, 105, 16555-16560.  
18348979 J.Cheung, C.A.Bingman, M.Reyngold, W.A.Hendrickson, and C.D.Waldburger (2008).
Crystal structure of a functional dimer of the PhoQ sensor domain.
  J Biol Chem, 283, 13762-13770.
PDB codes: 3bq8 3bqa
18701447 J.Cheung, and W.A.Hendrickson (2008).
Crystal Structures of C4-Dicarboxylate Ligand Complexes with Sensor Domains of Histidine Kinases DcuS and DctB.
  J Biol Chem, 283, 30256-30265.
PDB codes: 3by8 3by9
16679313 H.Irieda, M.Homma, M.Homma, and I.Kawagishi (2006).
Control of chemotactic signal gain via modulation of a pre-formed receptor array.
  J Biol Chem, 281, 23880-23886.  
16995896 J.C.Edwards, M.S.Johnson, and B.L.Taylor (2006).
Differentiation between electron transport sensing and proton motive force sensing by the Aer and Tsr receptors for aerotaxis.
  Mol Microbiol, 62, 823-837.  
16990134 M.B.Neiditch, M.J.Federle, A.J.Pompeani, R.C.Kelly, D.L.Swem, P.D.Jeffrey, B.L.Bassler, and F.M.Hughson (2006).
Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing.
  Cell, 126, 1095-1108.
PDB codes: 2hj9 2hje
16369945 M.D.Baker, P.M.Wolanin, and J.B.Stock (2006).
Signal transduction in bacterial chemotaxis.
  Bioessays, 28, 9.  
16714587 P.E.Stewart, X.Wang, D.M.Bueschel, D.R.Clifton, D.Grimm, K.Tilly, J.A.Carroll, J.J.Weis, and P.A.Rosa (2006).
Delineating the requirement for the Borrelia burgdorferi virulence factor OspC in the mammalian host.
  Infect Immun, 74, 3547-3553.  
16636062 T.Iwama, Y.Ito, H.Aoki, H.Sakamoto, S.Yamagata, K.Kawai, and I.Kawagishi (2006).
Differential recognition of citrate and a metal-citrate complex by the bacterial chemoreceptor Tcp.
  J Biol Chem, 281, 17727-17735.  
15653746 W.Zhang, J.S.Olson, and G.N.Phillips (2005).
Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis.
  Biophys J, 88, 2801-2814.  
15573139 G.H.Wadhams, and J.P.Armitage (2004).
Making sense of it all: bacterial chemotaxis.
  Nat Rev Mol Cell Biol, 5, 1024-1037.  
15187186 H.Szurmant, and G.W.Ordal (2004).
Diversity in chemotaxis mechanisms among the bacteria and archaea.
  Microbiol Mol Biol Rev, 68, 301-319.  
14731274 M.W.Bunn, and G.W.Ordal (2004).
Receptor conformational changes enhance methylesterase activity during chemotaxis by Bacillus subtilis.
  Mol Microbiol, 51, 721-728.  
15199056 Y.Suzuki, E.Moriyoshi, D.Tsuchiya, and H.Jingami (2004).
Negative cooperativity of glutamate binding in the dimeric metabotropic glutamate receptor subtype 1.
  J Biol Chem, 279, 35526-35534.  
12713898 D.D.Oprian (2003).
Phototaxis, chemotaxis and the missing link.
  Trends Biochem Sci, 28, 167-169.  
12775701 R.M.Weis, T.Hirai, A.Chalah, M.Kessel, P.J.Peters, and S.Subramaniam (2003).
Electron microscopic analysis of membrane assemblies formed by the bacterial chemotaxis receptor Tsr.
  J Bacteriol, 185, 3636-3643.  
12962628 W.Zhang, and G.N.Phillips (2003).
Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry.
  Structure, 11, 1097-1110.
PDB codes: 1or4 1or6
12672798 Y.Zhu, and M.Inouye (2003).
Analysis of the role of the EnvZ linker region in signal transduction using a chimeric Tar/EnvZ receptor protein, Tez1.
  J Biol Chem, 278, 22812-22819.  
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
12402035 J.Spudich (2002).
Spotlight on receptor/transducer interaction.
  Nat Struct Biol, 9, 797-799.  
11910034 M.L.Peach, G.L.Hazelbauer, and T.P.Lybrand (2002).
Modeling the transmembrane domain of bacterial chemoreceptors.
  Protein Sci, 11, 912-923.  
12119291 M.N.Levit, and J.B.Stock (2002).
Receptor methylation controls the magnitude of stimulus-response coupling in bacterial chemotaxis.
  J Biol Chem, 277, 36760-36765.  
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.  
12360255 P.De Meyts, and J.Whittaker (2002).
Structural biology of insulin and IGF1 receptors: implications for drug design.
  Nat Rev Drug Discov, 1, 769-783.  
12186970 S.H.Kim, W.Wang, and K.K.Kim (2002).
Dynamic and clustering model of bacterial chemotaxis receptors: structural basis for signaling and high sensitivity.
  Proc Natl Acad Sci U S A, 99, 11611-11615.  
12368857 V.I.Gordeliy, J.Labahn, R.Moukhametzianov, R.Efremov, J.Granzin, R.Schlesinger, G.Büldt, T.Savopol, A.J.Scheidig, J.P.Klare, and M.Engelhard (2002).
Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex.
  Nature, 419, 484-487.
PDB code: 1h2s
11230121 D.Kumaran, S.Eswaramoorthy, B.J.Luft, S.Koide, J.J.Dunn, C.L.Lawson, and S.Swaminathan (2001).
Crystal structure of outer surface protein C (OspC) from the Lyme disease spirochete, Borrelia burgdorferi.
  EMBO J, 20, 971-978.
PDB codes: 1f1m 1ggq
11504940 E.W.Yu, and D.E.Koshland (2001).
Propagating conformational changes over long (and short) distances in proteins.
  Proc Natl Acad Sci U S A, 98, 9517-9520.
PDB code: 1jmw
11553619 O.J.Murphy, X.Yi, R.M.Weis, and L.K.Thompson (2001).
Hydrogen exchange reveals a stable and expandable core within the aspartate receptor cytoplasmic domain.
  J Biol Chem, 276, 43262-43269.  
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.  
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.  
10660286 J.Stock, and M.Levit (2000).
Signal transduction: hair brains in bacterial chemotaxis.
  Curr Biol, 10, R11-R14.  
10671471 T.Iwama, K.I.Nakao, H.Nakazato, S.Yamagata, M.Homma, and I.Kawagishi (2000).
Mutational analysis of ligand recognition by tcp, the citrate chemoreceptor of Salmonella enterica serovar typhimurium.
  J Bacteriol, 182, 1437-1441.  
11084361 V.Anantharaman, and L.Aravind (2000).
Cache - a signaling domain common to animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors.
  Trends Biochem Sci, 25, 535-537.  
10489469 G.E.Dale, D.Kostrewa, B.Gsell, M.Stieger, and A.D'Arcy (1999).
Crystal engineering: deletion mutagenesis of the 24 kDa fragment of the DNA gyrase B subunit from Staphylococcus aureus.
  Acta Crystallogr D Biol Crystallogr, 55, 1626-1629.  
10481014 K.M.Ottemann, W.Xiao, Y.K.Shin, and D.E.Koshland (1999).
A piston model for transmembrane signaling of the aspartate receptor.
  Science, 285, 1751-1754.  
10350484 M.N.Levit, Y.Liu, and J.B.Stock (1999).
Mechanism of CheA protein kinase activation in receptor signaling complexes.
  Biochemistry, 38, 6651-6658.  
10425684 R.B.Bass, and J.J.Falke (1999).
The aspartate receptor cytoplasmic domain: in situ chemical analysis of structure, mechanism and dynamics.
  Structure, 7, 829-840.  
10467146 R.Reitzer, K.Gruber, G.Jogl, U.G.Wagner, H.Bothe, W.Buckel, and C.Kratky (1999).
Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights.
  Structure, 7, 891-902.
PDB codes: 1cb7 1ccw
9822812 M.N.Levit, Y.Liu, and J.B.Stock (1998).
Stimulus response coupling in bacterial chemotaxis: receptor dimers in signalling arrays.
  Mol Microbiol, 30, 459-466.  
9692965 S.L.Butler, and J.J.Falke (1998).
Cysteine and disulfide scanning reveals two amphiphilic helices in the linker region of the aspartate chemoreceptor.
  Biochemistry, 37, 10746-10756.  
9677402 X.N.Zhang, and J.L.Spudich (1998).
HtrI is a dimer whose interface is sensitive to receptor photoactivation and His-166 replacements in sensory rhodopsin I.
  J Biol Chem, 273, 19722-19728.  
9442881 J.J.Falke, R.B.Bass, S.L.Butler, S.A.Chervitz, and M.A.Danielson (1997).
The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes.
  Annu Rev Cell Dev Biol, 13, 457-512.  
9048553 J.Wang, Y.S.Balazs, and L.K.Thompson (1997).
Solid-state REDOR NMR distance measurements at the ligand site of a bacterial chemotaxis membrane receptor.
  Biochemistry, 36, 1699-1703.  
9407066 M.A.Danielson, R.B.Bass, and J.J.Falke (1997).
Cysteine and disulfide scanning reveals a regulatory alpha-helix in the cytoplasmic domain of the aspartate receptor.
  J Biol Chem, 272, 32878-32888.  
8942640 A.F.Kolodziej, T.Tan, and D.E.Koshland (1996).
Producing positive, negative, and no cooperativity by mutations at a single residue located at the subunit interface in the aspartate receptor of Salmonella typhimurium.
  Biochemistry, 35, 14782-14792.  
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.