3NB2

Crystal structure of E. coli O157:H7 effector protein NleL

• PDB DOI:  https://doi.org/10.2210/pdb3NB2/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-02 Released: 2010-10-27 
• Deposition Author(s): Lin, D.Y., Chen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.231 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Biochemical and Structural Studies of a HECT-like Ubiquitin Ligase from Escherichia coli O157:H7.

Lin, D.Y., Diao, J., Zhou, D., Chen, J.

(2011) J Biol Chem 286: 441-449

• PubMed: 20980253 
• DOI: https://doi.org/10.1074/jbc.M110.167643
• Primary Citation of Related Structures:  
  3NAW, 3NB2


• PubMed Abstract: 
  

Many microbial pathogens deliver effector proteins via the type III secretion system into infected host cells. Elucidating the function of these effectors is essential for our understanding of pathogenesis. Here, we describe biochemical and structural characterization of an effector protein (NleL) from Escherichia coli O157:H7, a widespread pathogen causing severe foodborne diseases. We show that NleL functionally and structurally mimics eukaryotic HECT E3 ligases and catalyzes formation of unanchored polyubiquitin chains using Lys(6) and Lys(48) linkage. The catalytic cysteine residue forms a thioester intermediate with ubiquitin. The structure of NleL contains two domains, a β-helix domain formed by pentapeptide repeats and a bilobed catalytic domain reminiscent of the N- and C-lobe architecture of HECT E3s. Six structures of NleL observed in two crystal forms revealed a large range of different positions of the C-lobe relative to the N-lobe, indicating that the helix linking the two lobes is extremely flexible. Comparing the structure of NleL with that of the Salmonella homolog SopA showed that the orientation of the C-lobes differ by as much as 108°, suggesting that large movements of the C-lobe may be required to facilitate the transfer of ubiquitin from E2 to the substrate. These results provide critical knowledge toward understanding the molecular mechanism by which pathogens utilize the host ubiquitination system during infection.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 283.2 kDa 
• Atom Count: 20,830 
• Modelled Residue Count: 2,448 
• Deposited Residue Count: 2,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
secreted effector protein	A, B, C, D	613	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: ECs1560, GI:13361024, espX7, ECs_1560 EC: 2.3.2.26
UniProt
Find proteins for A0A0H3JDV8 (Escherichia coli O157:H7) Explore A0A0H3JDV8  Go to UniProtKB:  A0A0H3JDV8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	LA [auth C], MA [auth C], R [auth A], YA [auth D], ZA [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
DTT	SA [auth C], W [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
SO4	AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], S [auth A], T [auth A], U [auth A], V [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth B], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], TA [auth D], UA [auth D], VA [auth D], WA [auth D], X [auth B], XA [auth D], Y [auth B], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.231 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.013	α = 90
b = 124.203	β = 107.6
c = 154.9	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-27 
Deposition Author(s): Lin, D.Y., Chen, J.

Revision History  

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description