2Z4I | pdb_00002z4i

Crystal structure of the Cpx pathway activator NlpE from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb2Z4I/pdb

• Classification: SIGNALING PROTEIN ACTIVATOR
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-18 Released: 2007-09-04 
• Deposition Author(s): Hirano, Y., Hossain, M.M., Takeda, K., Tokuda, H., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.270 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.240 (DCC) 

Literature

Structural Studies of the Cpx Pathway Activator NlpE on the Outer Membrane of Escherichia coli

Hirano, Y., Hossain, M.M., Takeda, K., Tokuda, H., Miki, K.

(2007) Structure 15: 963-976

• PubMed: 17698001 
• DOI: https://doi.org/10.1016/j.str.2007.06.014
• Primary Citation Related Structures: 
  2Z4H, 2Z4I


• PubMed 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.

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.69 kDa 
• Atom Count: 2,914 
• Modeled Residue Count: 384 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper homeostasis protein cutF	A, B	233	Escherichia coli	Mutation(s): 1  Gene Names: nlpE
UniProt
Find proteins for P40710 (Escherichia coli (strain K12)) Explore P40710  Go to UniProtKB:  P40710

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	C [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.270 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.240 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.422	α = 90
b = 121.422	β = 90
c = 84.456	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-04 
Deposition Author(s): Hirano, Y., Hossain, M.M., Takeda, K., Tokuda, H., Miki, K.

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Structure summary