Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.20 kDa 
• Atom Count: 3429 
• Modelled Residue Count: 403 
• Deposited Residue Count: 424 
• Unique protein chains: 1

3F0O

Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system

• PDB DOI: 10.2210/pdb3F0O/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-25 Released: 2008-11-11 
• Deposition Author(s): Lafrance-Vanasse, J., Lefebvre, M., Di Lello, P., Sygusch, J., Omichinski, J.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.208 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

Crystal Structures of the Organomercurial Lyase MerB in Its Free and Mercury-bound Forms: INSIGHTS INTO THE MECHANISM OF METHYLMERCURY DEGRADATION

Lafrance-Vanasse, J., Lefebvre, M., Di Lello, P., Sygusch, J., Omichinski, J.G.

(2009) J Biol Chem 284: 938-944

• PubMed: 19004822 
• DOI: 10.1074/jbc.M807143200
• Primary Citation of Related Structures:  
  3F0O, 3F0P, 3F2F, 3F2G, 3F2H


• PubMed Abstract: 
  

Bacteria resistant to methylmercury utilize two enzymes (MerA and MerB) to degrade methylmercury to the less toxic elemental mercury. The crucial step is the cleavage of the carbon-mercury bond of methylmercury by the organomercurial lyase (MerB). In this study, we determined high resolution crystal structures of MerB in both the free (1.76-A resolution) and mercury-bound (1.64-A resolution) states. The crystal structure of free MerB is very similar to the NMR structure, but important differences are observed when comparing the two structures. In the crystal structure, an amino-terminal alpha-helix that is not present in the NMR structure makes contact with the core region adjacent to the catalytic site. This interaction between the amino-terminal helix and the core serves to bury the active site of MerB. The crystal structures also provide detailed insights into the mechanism of carbon-mercury bond cleavage by MerB. The structures demonstrate that two conserved cysteines (Cys-96 and Cys-159) play a role in substrate binding, carbon-mercury bond cleavage, and controlled product (ionic mercury) release. In addition, the structures establish that an aspartic acid (Asp-99) in the active site plays a crucial role in the proton transfer step required for the cleavage of the carbon-mercury bond. These findings are an important step in understanding the mechanism of carbon-mercury bond cleavage by MerB.

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Organizational Affiliation: 

Department of Biochemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkylmercury lyase	A, B	212	Escherichia coli	Mutation(s): 0  Gene Names: merB EC: 4.99.1.2
UniProt
Find proteins for P77072 (Escherichia coli) Explore P77072  Go to UniProtKB:  P77072

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	C [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.208 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.71	α = 90
b = 89.947	β = 100.53
c = 52.167	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-25 
• Released Date: 2008-11-11 
Deposition Author(s): Lafrance-Vanasse, J., Lefebvre, M., Di Lello, P., Sygusch, J., Omichinski, J.G.

Revision History  

• Version 1.0: 2008-11-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance