1VJE

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

• PDB DOI: https://doi.org/10.2210/pdb1VJE/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-02-03 Released: 2004-02-10 
• Deposition Author(s): Structural GenomiX

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.215 
• R-Value Work: 0.188 

Literature

A Structural Genomics Approach to the Study of Quorum Sensing: Crystal Structures of Three LuxS Orthologs

Lewis, H.A., Furlong, E.B., Laubert, B., Eroshkina, G.A., Batiyenko, Y., Adams, J.M., Bergseid, M.G., Marsh, C.D., Peat, T.S., Sanderson, W.E., Sauder, J.M., Buchanan, S.G.

(2001) Structure 9: 527-537

• PubMed: 11435117 
• DOI: https://doi.org/10.1016/s0969-2126(01)00613-x
• Primary Citation of Related Structures:  
  1INN, 1J6V, 1J6W, 1J6X, 1VJE


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 

Structural GenomiX, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.37 kDa 
• Atom Count: 2,575 
• Modelled Residue Count: 299 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autoinducer-2 production protein LuxS	A, B	166	Deinococcus radiodurans	Mutation(s): 1  Gene Names: LUXS, DR2387 EC: 3.13.1
UniProt
Find proteins for Q9RRU8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RRU8  Go to UniProtKB:  Q9RRU8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MSE	D [auth A], E [auth A]	SELENOMETHIONINE C5 H11 N O2 Se RJFAYQIBOAGBLC-BYPYZUCNSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.215 
• R-Value Work: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.548	α = 90
b = 81.917	β = 102.81
c = 49.327	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
TRUNCATE	data reduction
REFMAC	refinement
CCP4	data scaling
TRUNCATE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-10 
Deposition Author(s): Structural GenomiX

Revision History  

• Version 1.0: 2004-02-10
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations