PDBsum entry 1vje

Hydrolase

PDB id: 1vje

Contents

Protein chains

149 a.a. *

Ligands

MSE ×2

Metals

_ZN ×2

Waters ×252

* Residue conservation analysis

PDB id:

1vje

Name:

Hydrolase

Title:

Crystal structure of a autoinducer-2 synthesis protein with bound selenomethionine

Structure:

Autoinducer-2 production protein luxs. Chain: a, b. Synonym: s-ribosylhomocysteinase, ai-2 synthesis protein. Engineered: yes

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Gene: luxs, dr2387. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.64Å R-factor: 0.188 R-free: 0.215

Authors:

Structural Genomix

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:

03-Feb-04 Release date: 10-Feb-04

Protein chains

Q9RRU8  (LUXS_DEIRA) -  S-ribosylhomocysteine lyase from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 158 a.a.

Struc: 149 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.4.1.21 - S-ribosylhomocysteine lyase.
• Pathway: Autoinducer AI-2 Biosynthesis
• Reaction: S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = (S)-4,5-dihydroxypentane-2,3- dione + L-homocysteine

S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = (S)-4,5-dihydroxypentane-2,3- dione + L-homocysteine (Bound ligand (Het Group name = MSE) matches with 70.00% similarity)

• Cofactor: Fe(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added 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.