3GKF | pdb_00003gkf

Crystal Structure of E. coli LsrF

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.229 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 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: https://doi.org/10.1371/journal.pone.0006820
  • Primary Citation Related Structures: 
    3GKF, 3GLC, 3GND

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 641.48 kDa 
  • Atom Count: 42,541 
  • Modeled Residue Count: 5,520 
  • Deposited Residue Count: 5,860 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aldolase lsrF293Escherichia coli K-12Mutation(s): 0 
Gene Names: b1517, JW1510, lsrF, yneB
EC: 4.1.2 (PDB Primary Data), 2.3.1.245 (UniProt)
UniProt
Find proteins for P76143 (Escherichia coli (strain K12))
Explore P76143 
Go to UniProtKB:  P76143
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76143
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.229 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.501α = 89.88
b = 104.61β = 79.31
c = 171.673γ = 89.61
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references
  • Version 1.5: 2024-04-03
    Changes: Refinement description