PDBsum entry: 1ie0

Structural genomics

PDB id: 1ie0

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

Protein chain

O34667  (LUXS_BACSU) -  S-ribosylhomocysteine lyase

Seq: 157 a.a.

Struc: 156 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 = L-homocysteine + (4S)-4,5- dihydroxypentan-2,3-dione

S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5- dihydroxypentan-2,3-dione (Bound ligand (Het Group name = GOL) matches with 66.67% similarity)

• Cofactor: Fe(2+)

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

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (5 terms)

reference

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.