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PDBsum entry 1ie0

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protein ligands metals links
Structural genomics PDB id
1ie0
Jmol
Contents
Protein chain
156 a.a. *
Ligands
GOL
Metals
_ZN
Waters ×187
* Residue conservation analysis
PDB id:
1ie0
Name: Structural genomics
Title: Crystal structure of luxs
Structure: Autoinducer-2 production protein luxs. Chain: a. Synonym: ai-2 synthesis protein. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: luxs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
1.60Å     R-factor:   0.174     R-free:   0.209
Authors: M.T.Hilgers,M.L.Ludwig
Key ref:
M.T.Hilgers and M.L.Ludwig (2001). Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site. Proc Natl Acad Sci U S A, 98, 11169-11174. PubMed id: 11553770 DOI: 10.1073/pnas.191223098
Date:
05-Apr-01     Release date:   03-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O34667  (LUXS_BACSU) -  S-ribosylhomocysteine lyase
Seq:
Struc:
157 a.a.
156 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!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1073/pnas.191223098 Proc Natl Acad Sci U S A 98:11169-11174 (2001)
PubMed id: 11553770  
 
 
Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site.
M.T.Hilgers, M.L.Ludwig.
 
  ABSTRACT  
 
The ability of bacteria to regulate gene expression in response to changes in cell density is termed quorum sensing. This behavior involves the synthesis and recognition of extracellular, hormone-like compounds known as autoinducers. Here we report the structure of an autoinducer synthase, LuxS from Bacillus subtilis, at 1.6-A resolution (R(free) = 0.204; R(work) = 0.174). LuxS is a homodimeric enzyme with a novel fold that incorporates two identical tetrahedral metal-binding sites. This metal center is composed of a Zn(2+) atom coordinated by two histidines, a cysteine, and a solvent molecule, and is reminiscent of active sites found in several peptidases and amidases. Although the nature of the autoinducer synthesized by LuxS cannot be deduced from the crystal structure, features of the putative active site suggest that LuxS might catalyze hydrolytic, but not proteolytic, cleavage of a small substrate. Our analysis represents a test of structure-based functional assignment.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. A stereoview of the Zn-ligand cluster and the putative active site of LuxS. Helix 1 bearing the HXXEH motif is at the Left; the chain from A118 to A132 underpins the zinc-binding site, covering the Zn ion (white) and its ligands. Invariant residues are drawn in ball-and-stick mode; A and B designate the two chains of the dimer. The conserved Asp-37 of the B chain lies beneath Arg-39 and is not labeled; Asn-44 is above Arg-39B at the border of the picture. The N-terminal 3[10] helix that may control entry to the active site is dark blue. In this view the substrate-binding cavity lies below the water bound to zinc and nestles against the strands of the -sheet from the B chain, seen at the back. Important interatomic distances in the active site region are as follows: Cys-84 S Zn, 4.86 Å; Arg-39 NH1 Cys-84 S , 4.04 Å; Glu-57 O 2 Zn, 4.69 Å.
Figure 3.
Fig. 3. The active site cavity in LuxS. This view is rotated 180° about the vertical from Fig. 2 for better display of the cavity and channel to solvent, which are outlined by the red mesh. Helix 1 with the HXXEH motif is now to the Right; strands from the B chain sheet (partly clipped) cover the cavity, and the N-terminal 3[10] helix (dark blue) is toward the reader. The cavity surface was generated with SURFNET (44).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20108028 R.S.Boyd (2010).
Heavy metal pollutants and chemical ecology: exploring new frontiers.
  J Chem Ecol, 36, 46-58.  
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.  
19754952 G.Kint, K.A.Sonck, G.Schoofs, D.De Coster, J.Vanderleyden, and S.C.De Keersmaecker (2009).
2D proteome analysis initiates new Insights on the Salmonella Typhimurium LuxS protein.
  BMC Microbiol, 9, 198.  
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.  
18956421 N.Ni, M.Li, J.Wang, and B.Wang (2009).
Inhibitors and antagonists of bacterial quorum sensing.
  Med Res Rev, 29, 65.  
19594442 S.Raina, D.D.Vizio, M.Odell, M.Clements, S.Vanhulle, and T.Keshavarz (2009).
Microbial quorum sensing: a tool or a target for antimicrobial therapy?
  Biotechnol Appl Biochem, 54, 65-84.  
19775890 T.Zang, B.W.Lee, L.M.Cannon, K.A.Ritter, S.Dai, D.Ren, T.K.Wood, and Z.S.Zhou (2009).
A naturally occurring brominated furanone covalently modifies and inactivates LuxS.
  Bioorg Med Chem Lett, 19, 6200-6204.  
19874060 T.Zang, S.Dai, D.Chen, B.W.Lee, S.Liu, B.L.Karger, and Z.S.Zhou (2009).
Chemical methods for the detection of protein N-homocysteinylation via selective reactions with aldehydes.
  Anal Chem, 81, 9065-9071.  
18956225 X.G.Han, and C.P.Lu (2009).
Detection of autoinducer-2 and analysis of the profile of luxS and pfs transcription in Streptococcus suis serotype 2.
  Curr Microbiol, 58, 146-152.  
17983264 C.H.Yeang, and D.Haussler (2007).
Detecting coevolution in and among protein domains.
  PLoS Comput Biol, 3, e211.  
17643872 C.Zhu, S.Feng, V.Sperandio, Z.Yang, T.E.Thate, J.B.Kaper, and E.C.Boedeker (2007).
The possible influence of LuxS in the in vivo virulence of rabbit enteropathogenic Escherichia coli.
  Vet Microbiol, 125, 313-322.  
  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.  
16740951 E.Lombardía, A.J.Rovetto, A.L.Arabolaza, and R.R.Grau (2006).
A LuxS-dependent cell-to-cell language regulates social behavior and development in Bacillus subtilis.
  J Bacteriol, 188, 4442-4452.  
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.  
16597969 S.Challan Belval, L.Gal, S.Margiewes, D.Garmyn, P.Piveteau, and J.Guzzo (2006).
Assessment of the roles of LuxS, S-ribosyl homocysteine, and autoinducer 2 in cell attachment during biofilm formation by Listeria monocytogenes EGD-e.
  Appl Environ Microbiol, 72, 2644-2650.  
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.  
15215334 D.A.Rodionov, A.G.Vitreschak, A.A.Mironov, and M.S.Gelfand (2004).
Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems.
  Nucleic Acids Res, 32, 3340-3353.  
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.  
15486712 N.Asanuma, T.Yoshii, and T.Hino (2004).
Molecular characterization and transcription of the luxS gene that encodes LuxS autoinducer 2 synthase in Streptococcus bovis.
  Curr Microbiol, 49, 366-371.  
15175279 S.C.Winans (2004).
Reciprocal regulation of bioluminescence and type III protein secretion in Vibrio harveyi and Vibrio parahaemolyticus in response to diffusible chemical signals.
  J Bacteriol, 186, 3674-3676.  
12654815 J.Merritt, F.Qi, S.D.Goodman, M.H.Anderson, and W.Shi (2003).
Mutation of luxS affects biofilm formation in Streptococcus mutans.
  Infect Immun, 71, 1972-1979.  
12758042 L.H.Zhang (2003).
Quorum quenching and proactive host defense.
  Trends Plant Sci, 8, 238-244.  
12819077 M.B.Jones, and M.J.Blaser (2003).
Detection of a luxS-signaling molecule in Bacillus anthracis.
  Infect Immun, 71, 3914-3919.  
12824325 T.A.Binkowski, S.Naghibzadeh, and J.Liang (2003).
CASTp: Computed Atlas of Surface Topography of proteins.
  Nucleic Acids Res, 31, 3352-3355.  
12117917 B.Stevenson, and K.Babb (2002).
LuxS-mediated quorum sensing in Borrelia burgdorferi, the lyme disease spirochete.
  Infect Immun, 70, 4099-4105.  
12472381 C.Giglione, and T.Meinnel (2002).
The situation on antimicrobial agents and chemotherapy in 2002: highlights of the 42nd ICAAC.
  Expert Opin Ther Targets, 6, 691-697.  
  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.  
12209001 P.E.Kolenbrander, R.N.Andersen, D.S.Blehert, P.G.Egland, J.S.Foster, and R.J.Palmer (2002).
Communication among oral bacteria.
  Microbiol Mol Biol Rev, 66, 486.  
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.