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PDBsum entry 2z4i

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protein ligands Protein-protein interface(s) links
Signaling protein activator PDB id
2z4i
Jmol
Contents
Protein chains
190 a.a. *
Ligands
P6G
SO4
Waters ×24
* Residue conservation analysis
PDB id:
2z4i
Name: Signaling protein activator
Title: Crystal structure of the cpx pathway activator nlpe from escherichia coli
Structure: Copper homeostasis protein cutf. Chain: a, b. Synonym: lipoprotein nlpe. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: nlpe. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.60Å     R-factor:   0.224     R-free:   0.270
Authors: Y.Hirano,M.M.Hossain,K.Takeda,H.Tokuda,K.Miki
Key ref:
Y.Hirano et al. (2007). Structural studies of the Cpx pathway activator NlpE on the outer membrane of Escherichia coli. Structure, 15, 963-976. PubMed id: 17698001 DOI: 10.1016/j.str.2007.06.014
Date:
18-Jun-07     Release date:   04-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P40710  (NLPE_ECOLI) -  Lipoprotein NlpE
Seq:
Struc:
236 a.a.
190 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     regulation of cell-substrate adhesion   1 term 

 

 
DOI no: 10.1016/j.str.2007.06.014 Structure 15:963-976 (2007)
PubMed id: 17698001  
 
 
Structural studies of the Cpx pathway activator NlpE on the outer membrane of Escherichia coli.
Y.Hirano, M.M.Hossain, K.Takeda, H.Tokuda, K.Miki.
 
  ABSTRACT  
 
NlpE, an outer membrane lipoprotein, functions during envelope stress responses in Gram-negative bacteria. In Escherichia coli, adhesion to abiotic surfaces has been reported to activate the Cpx pathway in an NlpE-dependent manner. External copper ions are also thought to activate the Cpx pathway mediated by NlpE. We determined the crystal structure of NlpE from E. coli at 2.6 A resolution. The structure showed that NlpE consists of two beta barrel domains. The N-terminal domain resembles the bacterial lipocalin Blc, and the C-terminal domain has an oligonucleotide/oligosaccharide-binding (OB) fold. From both biochemical analyses and the crystal structure, it can be deduced that the cysteine residues in the CXXC motif may be chemically active. Furthermore, two monomers in the asymmetric unit form an unusual 3D domain-swapped dimer. These findings indicate that tertiary and/or quaternary structural instability may be responsible for Cpx pathway activation.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Structural Properties of the N-Terminal Domain of NlpE
(A) Stereoscopic view of superposition between the N-terminal domain of NlpE (blue) and Blc (magenta, PDB code 1QWD). The rms distance of 68 Cα atoms is 2.2 Å.
(B) The hydrophobic environment of the cavity of the N-terminal β barrel. View from the upside of the cavity. The aromatic residues (Phe, Trp, and Tyr) and the hydrophobic residues (Ala, Cys, Gly, Ile, Leu, Met, Pro, and Val) are colored green and light green, respectively.
(C) The conserved residues of the cavity of the N-terminal β barrel. View from the same direction as in (B). The fully conserved residues are colored red. The strongly conserved residues and the weakly conserved residues are colored dark-orange and light orange, respectively. The fully conserved residues in type I NlpE homologs are colored dark pink (also see Figure 2).
Figure 8.
Figure 8. Structural Properties of the C-Terminal Domain of NlpE
(A) Stereoscopic view of superposition between the C-terminal domain of NlpE (orange) and the N-terminal domain (residues 1–104) of AspRS from E. coli (cyan, PDB code 1C0A). The rms distance of 57 Cα atoms is 1.6 Å.
(B) Surface of the C-terminal domain of NlpE colored red and blue, representing electrostatic potentials from −15 to +15 k[B]T (k[B], the Boltzmann constant; T, the absolute temperature). View from the same orientation as in (C).
(C) Surface of the N-terminal domain of AspRS colored the same as in (B). View from the DNA-binding site.
 
  The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 963-976) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944219 D.Das, P.Kozbial, G.W.Han, D.Carlton, L.Jaroszewski, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, M.C.Deller, L.Duan, K.Ellrott, M.A.Elsliger, D.Ernst, C.L.Farr, J.Feuerhelm, A.Grzechnik, J.C.Grant, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, S.S.Krishna, A.Kumar, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1254-1260.
PDB code: 3f1z
19943903 D.R.Buelow, and T.L.Raivio (2010).
Three (and more) component regulatory systems - auxiliary regulators of bacterial histidine kinases.
  Mol Microbiol, 75, 547-566.  
20230003 K.J.Rangan, Y.Y.Yang, G.Charron, and H.C.Hang (2010).
Rapid visualization and large-scale profiling of bacterial lipoproteins with chemical reporters.
  J Am Chem Soc, 132, 10628-10629.  
20211889 K.Nishino, S.Yamasaki, M.Hayashi-Nishino, and A.Yamaguchi (2010).
Effect of NlpE overproduction on multidrug resistance in Escherichia coli.
  Antimicrob Agents Chemother, 54, 2239-2243.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.