3GLC

Crystal Structure of E. coli LsrF in complex with Ribose-5-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.

Diaz, Z.Xavier, K.B.Miller, S.T.

(2009) Plos One 4: e6820-e6820

  • DOI: 10.1371/journal.pone.0006820
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated ...

    Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (alphabeta)(8)-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology with aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldolase lsrF
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
295Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: lsrF (yneB)
EC: 2.3.1.245
Find proteins for P76143 (Escherichia coli (strain K12))
Go to UniProtKB:  P76143
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R5P
Query on R5P

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
RIBOSE-5-PHOSPHATE
C5 H11 O8 P
PPQRONHOSHZGFQ-LMVFSUKVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 78.352α = 89.51
b = 105.451β = 79.79
c = 173.415γ = 90.34
Software Package:
Software NamePurpose
SCALAdata scaling
CBASSdata collection
PHASERphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance