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PDBsum entry 3gnd

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protein ligands Protein-protein interface(s) links
Lyase PDB id
3gnd
Jmol
Contents
Protein chains
(+ 14 more) 276 a.a. *
Ligands
5RP ×20
Waters ×376
* Residue conservation analysis
PDB id:
3gnd
Name: Lyase
Title: Crystal structure of e. Coli lsrf in complex with ribulose-5
Structure: Aldolase lsrf. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r fragment: uncharacterized aldolase lsrf. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: b1517, jw1510, lsrf, yneb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.90Å     R-factor:   0.197     R-free:   0.228
Authors: S.T.Miller,Z.C.Diaz
Key ref: Z.Diaz et al. (2009). The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF. PLoS One, 4, e6820. PubMed id: 19714241
Date:
17-Mar-09     Release date:   08-Sep-09    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P76143  (LSRF_ECOLI) -  Uncharacterized aldolase LsrF
Seq:
Struc:
291 a.a.
276 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
PLoS One 4:e6820 (2009)
PubMed id: 19714241  
 
 
The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.
Z.Diaz, K.B.Xavier, S.T.Miller.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20628367 I.M.Thijs, H.Zhao, A.De Weerdt, K.Engelen, D.De Coster, G.Schoofs, M.McClelland, J.Vanderleyden, K.Marchal, and S.C.De Keersmaecker (2010).
The AI-2-dependent regulator LsrR has a limited regulon in Salmonella Typhimurium.
  Cell Res, 20, 966-969.  
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