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PDBsum entry 1j6x

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protein ligands metals Protein-protein interface(s) links
Signaling protein PDB id
1j6x
Jmol
Contents
Protein chains
151 a.a. *
Ligands
MET ×2
Metals
_ZN ×2
Waters ×21
* Residue conservation analysis
PDB id:
1j6x
Name: Signaling protein
Title: Crystal structure of helicobacter pylori luxs
Structure: Autoinducer-2 production protein luxs. Chain: a, b. Synonym: ai-2 synthesis protein, conserved hypothetical protein jhp0097. Engineered: yes
Source: Helicobacter pylori. Organism_taxid: 210. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.38Å     R-factor:   0.219     R-free:   0.264
Authors: H.A.Lewis,E.B.Furlong,M.G.Bergseid,W.E.Sanderson, S.G.Buchanan
Key ref:
H.A.Lewis et al. (2001). A structural genomics approach to the study of quorum sensing: crystal structures of three LuxS orthologs. Structure, 9, 527-537. PubMed id: 11435117 DOI: 10.1016/S0969-2126(01)00613-X
Date:
14-May-01     Release date:   08-Jun-01    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9ZMW8  (LUXS_HELPJ) -  S-ribosylhomocysteine lyase
Seq:
Struc:
152 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.4.1.21  - S-ribosylhomocysteine lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Autoinducer AI-2 Biosynthesis
      Reaction: S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5- dihydroxypentan-2,3-dione
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine
=
L-homocysteine
Bound ligand (Het Group name = MET)
matches with 88.00% similarity
+ (4S)-4,5- dihydroxypentan-2,3-dione
      Cofactor: Fe(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     quorum sensing   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(01)00613-X Structure 9:527-537 (2001)
PubMed id: 11435117  
 
 
A structural genomics approach to the study of quorum sensing: crystal structures of three LuxS orthologs.
H.A.Lewis, E.B.Furlong, B.Laubert, G.A.Eroshkina, Y.Batiyenko, J.M.Adams, M.G.Bergseid, C.D.Marsh, T.S.Peat, W.E.Sanderson, J.M.Sauder, S.G.Buchanan.
 
  ABSTRACT  
 
BACKGROUND: Quorum sensing is the mechanism by which bacteria control gene expression in response to cell density. Two major quorum-sensing systems have been identified, system 1 and system 2, each with a characteristic signaling molecule (autoinducer-1, or AI-1, in the case of system 1, and AI-2 in system 2). The luxS gene is required for the AI-2 system of quorum sensing. LuxS and AI-2 have been described in both Gram-negative and Gram-positive bacterial species and have been shown to be involved in the expression of virulence genes in several pathogens. RESULTS: The structure of the LuxS protein from three different bacterial species with resolutions ranging from 1.8 A to 2.4 A has been solved using an X-ray crystallographic structural genomics approach. The structure of LuxS reported here is seen to have a new alpha-beta fold. In all structures, an equivalent homodimer is observed. A metal ion identified as zinc was seen bound to a Cys-His-His triad. Methionine was found bound to the protein near the metal and at the dimer interface. CONCLUSIONS: These structures provide support for a hypothesis that explains the in vivo action of LuxS. Specifically, acting as a homodimer, the protein binds a methionine analog, S-ribosylhomocysteine (SRH). The zinc atom is in position to cleave the ribose ring in a step along the synthesis pathway of AI-2.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Ball and Stick and Ribbon Diagram of the Substrate and Metal Binding SitesPotential hydrogen-bonding partners for the methionine ligand are shown by white dotted lines. Potential hydrogen bonding interactions with the zinc atom are also shown

 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 527-537) copyright 2001.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20704697 M.Bhattacharyya, and S.Vishveshwara (2010).
Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis.
  BMC Struct Biol, 10, 27.  
19099445 B.Gopishetty, J.Zhu, R.Rajan, A.J.Sobczak, S.F.Wnuk, C.E.Bell, and D.Pei (2009).
Probing the catalytic mechanism of S-ribosylhomocysteinase (LuxS) with catalytic intermediates and substrate analogues.
  J Am Chem Soc, 131, 1243-1250.  
19243584 M.Bhattacharyya, and S.Vishveshwara (2009).
Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks.
  BMC Struct Biol, 9, 8.  
19411415 M.Zhang, X.D.Jiao, Y.H.Hu, and L.Sun (2009).
Attenuation of Edwardsiella tarda virulence by small peptides that interfere with LuxS/autoinducer type 2 quorum sensing.
  Appl Environ Microbiol, 75, 3882-3890.  
18599834 M.Zhang, K.Sun, and L.Sun (2008).
Regulation of autoinducer 2 production and luxS expression in a pathogenic Edwardsiella tarda strain.
  Microbiology, 154, 2060-2069.  
  17869606 Y.Turovskiy, D.Kashtanov, B.Paskhover, and M.L.Chikindas (2007).
Quorum sensing: fact, fiction, and everything in between.
  Adv Appl Microbiol, 62, 191-234.  
16485279 C.Okada, Y.Maegawa, M.Yao, and I.Tanaka (2006).
Crystal structure of an RtcB homolog protein (PH1602-extein protein) from Pyrococcus horikoshii reveals a novel fold.
  Proteins, 63, 1119-1122.
PDB code: 1uc2
16897563 F.C.Petersen, N.A.Ahmed, A.Naemi, and A.A.Scheie (2006).
LuxS-mediated signalling in Streptococcus anginosus and its role in biofilm formation.
  Antonie Van Leeuwenhoek, 90, 109-121.  
17158701 J.E.González, and N.D.Keshavan (2006).
Messing with bacterial quorum sensing.
  Microbiol Mol Biol Rev, 70, 859-875.  
16459080 S.C.De Keersmaecker, K.Sonck, and J.Vanderleyden (2006).
Let LuxS speak up in AI-2 signaling.
  Trends Microbiol, 14, 114-119.  
15864263 A.Vendeville, K.Winzer, K.Heurlier, C.M.Tang, and K.R.Hardie (2005).
Making 'sense' of metabolism: autoinducer-2, LuxS and pathogenic bacteria.
  Nat Rev Microbiol, 3, 383-396.  
16021622 J.Badger, J.M.Sauder, J.M.Adams, S.Antonysamy, K.Bain, M.G.Bergseid, S.G.Buchanan, M.D.Buchanan, Y.Batiyenko, J.A.Christopher, S.Emtage, A.Eroshkina, I.Feil, E.B.Furlong, K.S.Gajiwala, X.Gao, D.He, J.Hendle, A.Huber, K.Hoda, P.Kearins, C.Kissinger, B.Laubert, H.A.Lewis, J.Lin, K.Loomis, D.Lorimer, G.Louie, M.Maletic, C.D.Marsh, I.Miller, J.Molinari, H.J.Muller-Dieckmann, J.M.Newman, B.W.Noland, B.Pagarigan, F.Park, T.S.Peat, K.W.Post, S.Radojicic, A.Ramos, R.Romero, M.E.Rutter, W.E.Sanderson, K.D.Schwinn, J.Tresser, J.Winhoven, T.A.Wright, L.Wu, J.Xu, and T.J.Harris (2005).
Structural analysis of a set of proteins resulting from a bacterial genomics project.
  Proteins, 60, 787-796.
PDB codes: 1o60 1o61 1o62 1o63 1o64 1o65 1o66 1o67 1o68 1o69 1o6b 1o6c 1o6d 1vgt 1vgu 1vgv 1vgw 1vgx 1vgy 1vgz 1vh0 1vh1 1vh2 1vh3 1vh4 1vh5 1vh6 1vh7 1vh8 1vh9 1vha 1vhc 1vhd 1vhe 1vhf 1vhg 1vhj 1vhk 1vhl 1vhm 1vho 1vhq 1vhs 1vht 1vhu 1vhv 1vhw 1vhx 1vhy 1vhz 1vi0 1vi1 1vi2 1vi3 1vi4 1vi5 1vi6 1vi8 1vi9 1via 1vic 1vim 1viq 1vis 1viu 1viv 1vix 1viy 1viz
15255890 K.M.Pappas, C.L.Weingart, and S.C.Winans (2004).
Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling.
  Mol Microbiol, 53, 755-769.  
  19498979 F.Schafer, A.Schafer, and K.Steinert (2002).
A highly specific system for efficient enzymatic removal of tags from recombinant proteins.
  J Biomol Tech, 13, 158-171.  
  19498977 F.Schafer, U.Romer, M.Emmerlich, J.Blumer, H.Lubenow, and K.Steinert (2002).
Automated high-throughput purification of 6xHis-tagged proteins.
  J Biomol Tech, 13, 131-142.  
11815235 L.Stewart, R.Clark, and C.Behnke (2002).
High-throughput crystallization and structure determination in drug discovery.
  Drug Discov Today, 7, 187-196.  
  12537600 M.P.DeLisa, and W.E.Bentley (2002).
Bacterial autoinduction: looking outside the cell for new metabolic engineering targets.
  Microb Cell Fact, 1, 5.  
12200329 O.M.Cloak, B.T.Solow, C.E.Briggs, C.Y.Chen, and P.M.Fratamico (2002).
Quorum sensing and production of autoinducer-2 in Campylobacter spp., Escherichia coli O157:H7, and Salmonella enterica serovar Typhimurium in foods.
  Appl Environ Microbiol, 68, 4666-4671.  
11931774 W.T.Watson, T.D.Minogue, D.L.Val, S.B.von Bodman, and M.E.Churchill (2002).
Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing.
  Mol Cell, 9, 685-694.
PDB codes: 1k4j 1kzf
11470577 R.N.Lawrence (2001).
News in brief.
  Drug Discov Today, 6, 759-762.  
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 code is shown on the right.