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PDBsum entry 1or6
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protein ligands Protein-protein interface(s) links
Signaling protein PDB id
1or6

 

 

 

 

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Contents
Protein chains
168 a.a. *
156 a.a. *
Ligands
HEM ×2
Waters ×185
* Residue conservation analysis
PDB id:
1or6
Name: Signaling protein
Title: Crystal structure of hemat sensor domain from b.Subtilis in the unliganded form
Structure: Heme-based aerotactic transducer hemat. Chain: a, b. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: yhfv. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.71Å     R-factor:   0.208     R-free:   0.329
Authors: W.Zhang,G.N.Phillips Jr.
Key ref:
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. PubMed id: 12962628 DOI: 10.1016/S0969-2126(03)00169-2
Date:
11-Mar-03     Release date:   23-Sep-03    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
O07621  (HEMAT_BACSU) -  Heme-based aerotactic transducer HemAT from Bacillus subtilis (strain 168)
Seq:
Struc: 		432 a.a.
168 a.a.
Protein chain
Pfam   ArchSchema ?
O07621  (HEMAT_BACSU) -  Heme-based aerotactic transducer HemAT from Bacillus subtilis (strain 168)
Seq:
Struc: 		432 a.a.
156 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0969-2126(03)00169-2 Structure 11:1097-1110 (2003)
PubMed id: 12962628  
 
 
Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry.
W.Zhang, G.N.Phillips.
 
  ABSTRACT  
 
Much is now known about chemotaxis signaling transduction for Escherichia coli and Salmonella typhimurium. The mechanism of chemotaxis of Bacillus subtilis is, in a sense, reversed. Attractant binding strengthens the activity of histidine kinase in B. subtilis, instead of an inhibition reaction. The HemAT from B. subtilis can detect oxygen and transmit the signal to regulatory proteins that control the direction of flagella rotation. We have determined the crystal structures of the HemAT sensor domain in liganded and unliganded forms at 2.15 A and 2.7 A resolution, respectively. The liganded structure reveals a highly symmetrical organization. Tyrosine70 shows distinct conformational changes on one subunit when ligands are removed. Our study suggests that disruption of the symmetry of HemAT plays an important role in initiating the chemotaxis signaling transduction cascade.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Molecular Structure of the HemAT Sensor Domain Represented with Ribbon Diagrams(A) Stereo view of the structure. The signaling domain would be located further down on the page.(B) Top view showing the flanking of the core helices, G and H, by the rest of the molecule. The helices are labeled corresponding to the nomenclature of the globin fold. Subunit A, cyan; subunit B, yellow.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1097-1110) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20361867 E.Geuens, D.Hoogewijs, M.Nardini, E.Vinck, A.Pesce, L.Kiger, A.Fago, L.Tilleman, S.De Henau, M.C.Marden, R.E.Weber, S.Van Doorslaer, J.Vanfleteren, L.Moens, M.Bolognesi, and S.Dewilde (2010).
Globin-like proteins in Caenorhabditis elegans: in vivo localization, ligand binding and structural properties.
  BMC Biochem, 11, 17.
PDB codes: 2wtg 2wth
19276084 H.Y.Cho, H.J.Cho, Y.M.Kim, J.I.Oh, and B.S.Kang (2009).
Structural Insight into the Heme-based Redox Sensing by DosS from Mycobacterium tuberculosis.
  J Biol Chem, 284, 13057-13067.
PDB codes: 2w3d 2w3e 2w3f 2w3g 2w3h
19246238 J.Green, J.C.Crack, A.J.Thomson, and N.E.LeBrun (2009).
Bacterial sensors of oxygen.
  Curr Opin Microbiol, 12, 145-151.  
18188182 M.Nardini, A.Pesce, L.Thijs, J.A.Saito, S.Dewilde, M.Alam, P.Ascenzi, M.Coletta, C.Ciaccio, L.Moens, and M.Bolognesi (2008).
Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity.
  EMBO Rep, 9, 157-163.
PDB codes: 2veb 2vee
18688409 S.Aono (2008).
Metal-containing sensor proteins sensing diatomic gas molecules.
  Dalton Trans, (), 3137-3146.  
18162468 S.F.El-Mashtoly, Y.Gu, H.Yoshimura, S.Yoshioka, S.Aono, and T.Kitagawa (2008).
Protein conformation changes of HemAT-Bs upon ligand binding probed by ultraviolet resonance Raman spectroscopy.
  J Biol Chem, 283, 6942-6949.  
17913492 H.Szurmant, R.A.White, and J.A.Hoch (2007).
Sensor complexes regulating two-component signal transduction.
  Curr Opin Struct Biol, 17, 706-715.  
17628132 K.Wuichet, R.P.Alexander, and I.B.Zhulin (2007).
Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis.
  Methods Enzymol, 422, 1.  
17925395 L.Thijs, E.Vinck, A.Bolli, F.Trandafir, X.Wan, D.Hoogewijs, M.Coletta, A.Fago, R.E.Weber, S.Van Doorslaer, P.Ascenzi, M.Alam, L.Moens, and S.Dewilde (2007).
Characterization of a globin-coupled oxygen sensor with a gene-regulating function.
  J Biol Chem, 282, 37325-37340.  
16699195 M.Makino, H.Sugimoto, H.Sawai, N.Kawada, K.Yoshizato, and Y.Shiro (2006).
High-resolution structure of human cytoglobin: identification of extra N- and C-termini and a new dimerization mode.
  Acta Crystallogr D Biol Crystallogr, 62, 671-677.
PDB code: 2dc3
16600051 S.N.Vinogradov, D.Hoogewijs, X.Bailly, R.Arredondo-Peter, J.Gough, S.Dewilde, L.Moens, and J.R.Vanfleteren (2006).
A phylogenomic profile of globins.
  BMC Evol Biol, 6, 31.  
15642260 E.A.Sickmier, D.Brekasis, S.Paranawithana, J.B.Bonanno, M.S.Paget, S.K.Burley, and C.L.Kielkopf (2005).
X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing.
  Structure, 13, 43-54.
PDB code: 1xcb
16135523 J.J.Miranda, D.H.Maillett, J.Soman, and J.S.Olson (2005).
Thermoglobin, oxygen-avid hemoglobin in a bacterial hyperthermophile.
  J Biol Chem, 280, 36754-36761.  
16301540 J.W.Murray, O.Delumeau, and R.J.Lewis (2005).
Structure of a nonheme globin in environmental stress signaling.
  Proc Natl Acad Sci U S A, 102, 17320-17325.
PDB code: 2bnl
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.  
15187186 H.Szurmant, and G.W.Ordal (2004).
Diversity in chemotaxis mechanisms among the bacteria and archaea.
  Microbiol Mol Biol Rev, 68, 301-319.  
15550941 J.Green, and M.S.Paget (2004).
Bacterial redox sensors.
  Nat Rev Microbiol, 2, 954-966.  
15096613 T.A.Freitas, S.Hou, E.M.Dioum, J.A.Saito, J.Newhouse, G.Gonzalez, M.A.Gilles-Gonzalez, and M.Alam (2004).
Ancestral hemoglobins in Archaea.
  Proc Natl Acad Sci U S A, 101, 6675-6680.  
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.

 

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