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PDBsum entry 1xbn
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Signaling protein PDB id
1xbn

 

 

 

 

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Contents
Protein chain
195 a.a. *
Ligands
OXY-HEM
Waters ×11
* Residue conservation analysis
PDB id:
1xbn
Name: Signaling protein
Title: Crystal structure of a bacterial nitric oxide sensor: an ortholog of mammalian soluble guanylate cyclase heme domain
Structure: Methyl-accepting chemotaxis protein. Chain: a. Engineered: yes
Source: Thermoanaerobacter tengcongensis mb4. Organism_taxid: 273068. Strain: mb4t. Gene: tar4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.50Å     R-factor:   0.265     R-free:   0.291
Authors: P.Nioche,C.S.Raman
Key ref:
P.Nioche et al. (2004). Femtomolar sensitivity of a NO sensor from Clostridium botulinum. Science, 306, 1550-1553. PubMed id: 15472039 DOI: 10.1126/science.1103596
Date:
30-Aug-04     Release date:   07-Sep-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8RBX6  (Q8RBX6_CALS4) -  Methyl-accepting chemotaxis protein from Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)
Seq:
Struc: 		 
Seq:
Struc: 		602 a.a.
195 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1126/science.1103596 Science 306:1550-1553 (2004)
PubMed id: 15472039  
 
 
Femtomolar sensitivity of a NO sensor from Clostridium botulinum.
P.Nioche, V.Berka, J.Vipond, N.Minton, A.L.Tsai, C.S.Raman.
 
  ABSTRACT  
 
Nitric oxide (NO) is extremely toxic to Clostridium botulinum, but its molecular targets are unknown. Here, we identify a heme protein sensor (SONO) that displays femtomolar affinity for NO. The crystal structure of the SONO heme domain reveals a previously undescribed fold and a strategically placed tyrosine residue that modulates heme-nitrosyl coordination. Furthermore, the domain architecture of a SONO ortholog cloned from Chlamydomonas reinhardtii indicates that NO signaling through cyclic guanosine monophosphate arose before the origin of multicellular eukaryotes. Our findings have broad implications for understanding bacterial responses to NO, as well as for the activation of mammalian NO-sensitive guanylyl cyclase.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Three-dimensional structure of TT-SONO[HD]. Ribbon diagram depicts residues 1 to 181 of the protein. The heme prosthetic group (red) and the histidine coordinating its iron are also shown. 		Figure 3.
Fig. 3. Omit difference electron density map (F[obs] - F[calc]) of the heme pocket. Maps are shown at 3 level. Oxygen ligand density is in blue. Dotted line indicates that the phenolic -OH of Tyr140 is within hydrogen-bonding distance of the oxygen ligand.
 
  The above figures are reprinted by permission from the AAAs: Science (2004, 306, 1550-1553) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21354424 B.Goblirsch, R.C.Kurker, B.R.Streit, C.M.Wilmot, and J.L.DuBois (2011).
Chlorite dismutases, DyPs, and EfeB: 3 microbial heme enzyme families comprise the CDE structural superfamily.
  J Mol Biol, 408, 379-398.  
20162612 C.Olea, M.A.Herzik, J.Kuriyan, and M.A.Marletta (2010).
Structural insights into the molecular mechanism of H-NOX activation.
  Protein Sci, 19, 881-887.
PDB codes: 3lah 3lai
20063108 F.Zhong, H.Wang, T.Ying, Z.X.Huang, and X.Tan (2010).
Efficient expression of human soluble guanylate cyclase in Escherichia coli and its signaling-related interaction with nitric oxide.
  Amino Acids, 39, 399-408.  
20353168 M.Ibrahim, E.R.Derbyshire, M.A.Marletta, and T.G.Spiro (2010).
Probing soluble guanylate cyclase activation by CO and YC-1 using resonance Raman spectroscopy.
  Biochemistry, 49, 3815-3823.  
20657650 T.Haase, N.Haase, J.R.Kraehling, and S.Behrends (2010).
Fluorescent fusion proteins of soluble guanylyl cyclase indicate proximity of the heme nitric oxide domain and catalytic domain.
  PLoS One, 5, e11617.  
20105301 X.Ma, A.Beuve, and F.van den Akker (2010).
Crystal structure of the signaling helix coiled-coil domain of the beta1 subunit of the soluble guanylyl cyclase.
  BMC Struct Biol, 10, 2.
PDB code: 3hls
19439177 F.Murad, and R.Barber (2009).
A hypothesis about cellular signaling with nitric oxide in the earliest life forms in evolution.
  Free Radic Biol Med, 47, 1325-1327.  
19656291 J.D.Partridge, D.M.Bodenmiller, M.S.Humphrys, and S.Spiro (2009).
NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility.
  Mol Microbiol, 73, 680-694.  
19161328 N.J.Silvernail, A.Barabanschikov, J.T.Sage, B.C.Noll, and W.R.Scheidt (2009).
Mapping NO movements in crystalline [Fe(Porph)(NO)(1-MeIm)].
  J Am Chem Soc, 131, 2131-2140.  
19653642 R.Tran, E.M.Boon, M.A.Marletta, and R.A.Mathies (2009).
Resonance Raman spectra of an O2-binding H-NOX domain reveal heme relaxation upon mutation.
  Biochemistry, 48, 8568-8577.  
19918063 W.K.Erbil, M.S.Price, D.E.Wemmer, and M.A.Marletta (2009).
A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation.
  Proc Natl Acad Sci U S A, 106, 19753-19760.
PDB codes: 2kii 2kil
18682395 C.E.Monk, B.M.Pearson, F.Mulholland, H.K.Smith, and R.K.Poole (2008).
Oxygen- and NssR-dependent globin expression and enhanced iron acquisition in the response of campylobacter to nitrosative stress.
  J Biol Chem, 283, 28413-28425.  
18274790 C.Xu, and G.S.Thomas (2008).
Ambidentate H-bonding by heme-bound NO: structural and spectral effects of -O versus -N H-bonding.
  J Biol Inorg Chem, 13, 613-621.  
18316370 I.Gusarov, M.Starodubtseva, Z.Q.Wang, L.McQuade, S.J.Lippard, D.J.Stuehr, and E.Nudler (2008).
Bacterial nitric-oxide synthases operate without a dedicated redox partner.
  J Biol Chem, 283, 13140-13147.  
18842118 J.A.Winger, E.R.Derbyshire, M.H.Lamers, M.A.Marletta, and J.Kuriyan (2008).
The crystal structure of the catalytic domain of a eukaryotic guanylate cyclase.
  BMC Struct Biol, 8, 42.
PDB code: 3et6
18672900 K.A.Marvin, R.L.Kerby, H.Youn, G.P.Roberts, and J.N.Burstyn (2008).
The transcription regulator RcoM-2 from Burkholderia xenovorans is a cysteine-ligated hemoprotein that undergoes a redox-mediated ligand switch.
  Biochemistry, 47, 9016-9028.  
18331637 K.Manikandan, D.Pal, S.Ramakumar, N.E.Brener, S.S.Iyengar, and G.Seetharaman (2008).
Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments.
  Genome Biol, 9, R52.  
18688409 S.Aono (2008).
Metal-containing sensor proteins sensing diatomic gas molecules.
  Dalton Trans, (), 3137-3146.  
  19032089 T.Spiro (2008).
A twist on heme signaling.
  ACS Chem Biol, 3, 673-675.  
18515359 X.Hu, L.B.Murata, A.Weichsel, J.L.Brailey, S.A.Roberts, A.Nighorn, and W.R.Montfort (2008).
Allostery in recombinant soluble guanylyl cyclase from Manduca sexta.
  J Biol Chem, 283, 20968-20977.  
18006497 X.Ma, N.Sayed, P.Baskaran, A.Beuve, and F.van den Akker (2008).
PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure.
  J Biol Chem, 283, 1167-1178.
PDB codes: 2p04 2p08
17550789 D.A.Landfried, D.A.Vuletich, M.P.Pond, and J.T.Lecomte (2007).
Structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins.
  Gene, 398, 12-28.  
  19122779 D.B.Morton, and A.Vermehren (2007).
Soluble Guanylyl Cyclases in Invertebrates: Targets for NO and O(2).
  Adv Exp Biol, 1, 65-82.  
17329176 D.Y.Boudko (2007).
Bioanalytical profile of the L-arginine/nitric oxide pathway and its evaluation by capillary electrophoresis.
  J Chromatogr B Analyt Technol Biomed Life Sci, 851, 186-210.  
17318598 M.A.Carrondo, I.Bento, P.M.Matias, and P.F.Lindley (2007).
Crystallographic evidence for dioxygen interactions with iron proteins.
  J Biol Inorg Chem, 12, 429-442.  
17988156 M.S.Price, L.Y.Chao, and M.A.Marletta (2007).
Shewanella oneidensis MR-1 H-NOX regulation of a histidine kinase by nitric oxide.
  Biochemistry, 46, 13677-13683.  
17519437 M.Sebaihia, M.W.Peck, N.P.Minton, N.R.Thomson, M.T.Holden, W.J.Mitchell, A.T.Carter, S.D.Bentley, D.R.Mason, L.Crossman, C.J.Paul, A.Ivens, M.H.Wells-Bennik, I.J.Davis, A.M.Cerdeño-Tárraga, C.Churcher, M.A.Quail, T.Chillingworth, T.Feltwell, A.Fraser, I.Goodhead, Z.Hance, K.Jagels, N.Larke, M.Maddison, S.Moule, K.Mungall, H.Norbertczak, E.Rabbinowitsch, M.Sanders, M.Simmonds, B.White, S.Whithead, and J.Parkhill (2007).
Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes.
  Genome Res, 17, 1082-1092.  
17313521 S.Spiro (2007).
Regulators of bacterial responses to nitric oxide.
  FEMS Microbiol Rev, 31, 193-211.  
17215864 X.Ma, N.Sayed, A.Beuve, and F.van den Akker (2007).
NO and CO differentially activate soluble guanylyl cyclase via a heme pivot-bend mechanism.
  EMBO J, 26, 578-588.
PDB codes: 2o09 2o0c 2o0g
16955067 O.V.Evgenov, P.Pacher, P.M.Schmidt, G.Haskó, H.H.Schmidt, and J.P.Stasch (2006).
NO-independent stimulators and activators of soluble guanylate cyclase: discovery and therapeutic potential.
  Nat Rev Drug Discov, 5, 755-768.  
16410360 R.W.Clark, N.D.Lanz, A.J.Lee, R.L.Kerby, G.P.Roberts, and J.N.Burstyn (2006).
Unexpected NO-dependent DNA binding by the CooA homolog from Carboxydothermus hydrogenoformans.
  Proc Natl Acad Sci U S A, 103, 891-896.  
16530415 S.P.Cary, J.A.Winger, E.R.Derbyshire, and M.A.Marletta (2006).
Nitric oxide signaling: no longer simply on or off.
  Trends Biochem Sci, 31, 231-239.  
17015012 T.L.Poulos (2006).
Soluble guanylate cyclase.
  Curr Opin Struct Biol, 16, 736-743.  
16125437 E.M.Boon, and M.A.Marletta (2005).
Ligand discrimination in soluble guanylate cyclase and the H-NOX family of heme sensor proteins.
  Curr Opin Chem Biol, 9, 441-446.  
16407994 E.M.Boon, S.H.Huang, and M.A.Marletta (2005).
A molecular basis for NO selectivity in soluble guanylate cyclase.
  Nat Chem Biol, 1, 53-59.  
16045618 K.T.Elvers, S.M.Turner, L.M.Wainwright, G.Marsden, J.Hinds, J.A.Cole, R.K.Poole, C.W.Penn, and S.F.Park (2005).
NssR, a member of the Crp-Fnr superfamily from Campylobacter jejuni, regulates a nitrosative stress-responsive regulon that includes both a single-domain and a truncated haemoglobin.
  Mol Microbiol, 57, 735-750.  
  16511163 S.Schneider, and M.Paoli (2005).
Crystallization and preliminary X-ray diffraction analysis of the haem-binding protein HemS from Yersinia enterocolitica.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 802-805.  
16407983 T.G.Spiro (2005).
Pulling NO out of thin air.
  Nat Chem Biol, 1, 6-7.  
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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