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23  structures 2619  species 1  interaction 2731  sequences 2  architectures

Family: LuxS (PF02664)

Summary: S-Ribosylhomocysteinase (LuxS)

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This is the Wikipedia entry entitled "S-ribosylhomocysteine lyase". More...

S-ribosylhomocysteine lyase Edit Wikipedia article

S-ribosylhomocysteine lyase
Identifiers
EC number 4.4.1.21
CAS number 37288-63-4
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
S-Ribosylhomocysteinase (LuxS)
PDB 1joe EBI.jpg
crystal structure of autoinducer-2 production protein (luxs) from Haemophilus influenzae
Identifiers
Symbol LuxS
Pfam PF02664
Pfam clan CL0094
InterPro IPR003815
SCOP 1inn
SUPERFAMILY 1inn

In enzymology, a S-ribosylhomocysteine lyase (EC 4.4.1.21) is an enzyme that catalyzes the chemical reaction

S-(5-deoxy-D-ribos-5-yl)-L-homocysteine \rightleftharpoons L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione

Hence, this enzyme has one substrate, S-(5-deoxy-D-ribos-5-yl)-L-homocysteine, and two products, L-homocysteine and (4S)-4,5-dihydroxypentan-2,3-dione.

This enzyme belongs to the family of lyases, specifically the class of carbon-sulfur lyases. The systematic name of this enzyme class is S-(5-deoxy-D-ribos-5-yl)-L-homocysteine L-homocysteine-lyase [(4S)-4,5-dihydroxypentan-2,3-dione-forming]. Other names in common use include S-ribosylhomocysteinase, and LuxS. This enzyme participates in methionine metabolism.

Furthermore, LuxS is involved in the synthesis of autoinducer AI-2 (autoinducer-2), which is plays a role in quorum sensing in a certain number of bacterial species. LuxS converts S-ribosylhomocysteine to homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD); DPD can then spontaneously cyclisize to active AI-2.[1][2] AI-2 is a signalling molecule that is believe to act in interspecies communication by regulating niche-specific genes with diverse functions in various bacteria, often in response to population density. However, an unequivocally AI-2 related behavior was found to be restricted primarily to bacteria bearing known AI-2 receptor genes.[3] Thus, while it is certainly true that some bacteria can respond to AI-2, it is doubtful that it is always being produced for purposes of signalling. LuxS is a homodimeric iron-dependent metalloenzyme containing two identical tetrahedral metal-binding sites similar to those found in peptidases and amidases.[4]

Structural studies

As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 1JQW, 2FQO, and 2FQT.

References

  1. ^ van Houdt R, Moons P, Jansen A, Vanoirbeek K, Michiels CW (September 2006). "Isolation and functional analysis of luxS in Serratia plymuthica RVH1". FEMS Microbiol. Lett. 262 (2): 201–9. doi:10.1111/j.1574-6968.2006.00391.x. PMID 16923076. 
  2. ^ Zhu J, Patel R, Pei D (August 2004). "Catalytic mechanism of S-ribosylhomocysteinase (LuxS): stereochemical course and kinetic isotope effect of proton transfer reactions". Biochemistry 43 (31): 10166–72. doi:10.1021/bi0491088. PMID 15287744. 
  3. ^ Rezzonico, F.; Duffy, B. (2008). "Lack of genomic evidence of AI-2 receptors suggests a non-quorum sensing role for LuxS in most bacteria". BMC Microbiology 8: 154. PMID 18803868. 
  4. ^ Rajan R, Zhu J, Hu X, Pei D, Bell CE (March 2005). "Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate". Biochemistry 44 (10): 3745–53. doi:10.1021/bi0477384. PMID 15751951. 

Further reading

This article incorporates text from the public domain Pfam and InterPro IPR003815


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

S-Ribosylhomocysteinase (LuxS) Provide feedback

This family consists of the LuxS protein involved in autoinducer AI2 synthesis and its hypothetical relatives. S-ribosylhomocysteinase (LuxS) catalyses the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum sensing molecule.

Literature references

  1. Surette MG, Miller MB, Bassler BL; , Proc Natl Acad Sci U S A 1999;96:1639-1644.: Quorum sensing in Escherichia coli, Salmonella typhimurium, and Vibrio harveyi: a new family of genes responsible for autoinducer production. PUBMED:9990077 EPMC:9990077

  2. Zhu J, Patel R, Pei D; , Biochemistry 2004;43:10166-10172.: Catalytic mechanism of S-ribosylhomocysteinase (LuxS): stereochemical course and kinetic isotope effect of proton transfer reactions. PUBMED:15287744 EPMC:15287744

  3. Zhu J, Hu X, Dizin E, Pei D; , J Am Chem Soc 2003;125:13379-13381.: Catalytic mechanism of S-ribosylhomocysteinase (LuxS): direct observation of ketone intermediates by 13C NMR spectroscopy. PUBMED:14583032 EPMC:14583032

  4. Zhu J, Dizin E, Hu X, Wavreille AS, Park J, Pei D; , Biochemistry 2003;42:4717-4726.: S-Ribosylhomocysteinase (LuxS) is a mononuclear iron protein. PUBMED:12705835 EPMC:12705835


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003815

In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. Quorum-sensing bacteria produce, release, and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. For example, enteric bacteria use quorum sensing to regulate several traits that allow them to establish and maintain infection in their host, including motility, biofilm formation, and virulence-specific genes [PUBMED:17133078]. The LuxS/AI-2 system is one of several quorum sensing mechanisms. AI-2 (autoinducer-2) is a signalling molecule that functions in interspecies communication by regulating niche-specific genes with diverse functions in various bacteria, often in response to population density. LuxS (S-ribosylhomocysteinase; EC) is an autoinducer-production protein that has a metabolic function as a component of the activated methyl cycle. LuxS converts S-ribosylhomocysteine to homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD); DPD can then spontaneously cyclise to active AI-2 [PUBMED:16923076, PUBMED:15287744]. LuxS is a homodimeric iron-dependent metalloenzyme containing two identical tetrahedral metal-binding sites similar to those found in peptidases and amidases [PUBMED:15751951].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Peptidase_ME (CL0094), which has the following description:

All members of this clan are characterised by a HXXEH motif, which is is involved in zinc binding. Furthermore all members adopt an alpha and beta fold. More specifically, there us a four to six stranded antiparallel beta sheet surrounded by five helices. However, LuxS (PFAM:PF02664) is not a peptidase, although its hydrolytic mechanism of catalysis appears to be conserved [1].

The clan contains the following 4 members:

LuxS Peptidase_M16 Peptidase_M16_C Peptidase_M44

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(5)
Full
(2731)
Representative proteomes NCBI
(1250)
Meta
(26)
RP15
(74)
RP35
(166)
RP55
(239)
RP75
(302)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(5)
Full
(2731)
Representative proteomes NCBI
(1250)
Meta
(26)
RP15
(74)
RP35
(166)
RP55
(239)
RP75
(302)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(5)
Full
(2731)
Representative proteomes NCBI
(1250)
Meta
(26)
RP15
(74)
RP35
(166)
RP55
(239)
RP75
(302)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: COG1854
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A, Adamkewicz J
Number in seed: 5
Number in full: 2731
Average length of the domain: 152.40 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 95.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.2 20.2
Trusted cut-off 21.0 21.0
Noise cut-off 19.6 18.9
Model length: 157
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

LuxS

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the LuxS domain has been found. There are 23 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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