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PDBsum entry 1ycl

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protein ligands metals links
Hydrolase PDB id
1ycl
Jmol
Contents
Protein chain
154 a.a. *
Ligands
SO4
KRI
Metals
_CO
Waters ×103
* Residue conservation analysis
PDB id:
1ycl
Name: Hydrolase
Title: Crystal structure of b. Subtilis luxs in complex with a cata ketone intermediate
Structure: S-ribosylhomocysteinase. Chain: a. Synonym: autoinducer-2 production protein luxs, ai-2 synthe 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:
1.80Å     R-factor:   0.225     R-free:   0.256
Authors: R.Rajan,J.Zhu,X.Hu,D.Pei,C.E.Bell
Key ref:
R.Rajan et al. (2005). Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate. Biochemistry, 44, 3745-3753. PubMed id: 15751951 DOI: 10.1021/bi0477384
Date:
22-Dec-04     Release date:   15-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O34667  (LUXS_BACSU) -  S-ribosylhomocysteine lyase
Seq:
Struc:
157 a.a.
154 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
Bound ligand (Het Group name = KRI)
corresponds exactly
= L-homocysteine
+ (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     metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi0477384 Biochemistry 44:3745-3753 (2005)
PubMed id: 15751951  
 
 
Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate.
R.Rajan, J.Zhu, X.Hu, D.Pei, C.E.Bell.
 
  ABSTRACT  
 
S-Ribosylhomocysteinase (LuxS) is an Fe(2+)-dependent metalloenzyme that catalyzes the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine (Hcys) and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum-sensing molecule. The proposed mechanism involves an initial metal-catalyzed aldose-ketose isomerization reaction, which results in the migration of the ribose carbonyl group from its C1 to C2 position and the formation of a 2-ketone intermediate. A repetition of the isomerization reaction shifts the carbonyl group to the C3 position. Subsequent beta-elimination reaction at the C4 and C5 positions completes the catalytic cycle. In this work, a catalytically inactive mutant (C84A) of Co(2+)-substituted Bacillus subtilis LuxS was cocrystallized with the 2-ketone intermediate and the structure was determined to 1.8 A resolution. The structure reveals that the C2 carbonyl oxygen is directly coordinated with the metal ion, providing strong support for the proposed Lewis acid function of the metal ion during catalysis. Cys-84 and Glu-57 are optimally positioned to act as general acids/bases during the isomerization and elimination reactions. In addition, Ser-6, His-11, and Arg-39 are involved in substrate/ intermediate binding through hydrogen bonding interactions. The above conclusions are further confirmed by site-directed mutagenesis and visible absorption spectroscopic studies.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264316 P.Plummer, J.Zhu, M.Akiba, D.Pei, and Q.Zhang (2011).
Identification of a key amino acid of LuxS involved in AI-2 production in Campylobacter jejuni.
  PLoS One, 6, e15876.  
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.  
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.  
19682914 S.F.Wnuk, J.Robert, A.J.Sobczak, B.P.Meyers, V.L.Malladi, J.Zhu, B.Gopishetty, and D.Pei (2009).
Inhibition of S-ribosylhomocysteinase (LuxS) by substrate analogues modified at the ribosyl C-3 position.
  Bioorg Med Chem, 17, 6699-6706.  
18375129 S.F.Wnuk, J.Lalama, C.A.Garmendia, J.Robert, J.Zhu, and D.Pei (2008).
S-Ribosylhomocysteine analogues with the carbon-5 and sulfur atoms replaced by a vinyl or (fluoro)vinyl unit.
  Bioorg Med Chem, 16, 5090-5102.  
17143597 R.Vilchez, A.Lemme, V.Thiel, S.Schulz, H.Sztajer, and I.Wagner-Döbler (2007).
Analysing traces of autoinducer-2 requires standardization of the Vibrio harveyi bioassay.
  Anal Bioanal Chem, 387, 489-496.  
  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.  
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.  
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.