Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.06 kDa 
• Atom Count: 1466 
• Modelled Residue Count: 192 
• Deposited Residue Count: 212 
• Unique protein chains: 1

1S6L

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

• PDB DOI: 10.2210/pdb1S6L/pdb
• BMRB: 6047

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-01-25 Released: 2005-04-19 
• Deposition Author(s): Di Lello, P., Benison, G.C., Valafar, H., Pitts, K.E., Summers, A.O., Legault, P., Omichinski, J.G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 55 
• Conformers Submitted: 20 
• Selection Criteria: The submitted models are the 20 structures with no upper bound violation greater that 0.3 armstrongs and no dihedral angle restraint violation greater than 2 degrees and with the lowest energies. 

Literature

NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system.

Di Lello, P., Benison, G.C., Valafar, H., Pitts, K.E., Summers, A.O., Legault, P., Omichinski, J.G.

(2004) Biochemistry 43: 8322-8332

• PubMed: 15222745 
• DOI: 10.1021/bi049669z
• Primary Citation of Related Structures:  
  1S6L


• PubMed Abstract: 
  

Mercury resistant bacteria have developed a system of two enzymes (MerA and MerB), which allows them to efficiently detoxify both ionic and organomercurial compounds. The organomercurial lyase (MerB) catalyzes the protonolysis of the carbon-mercury bond resulting in the formation of ionic mercury and a reduced hydrocarbon. The ionic mercury [Hg(II)] is subsequently reduced to the less reactive elemental mercury [Hg(0)] by a specific mercuric reductase (MerA). To better understand MerB's unique enzymatic activity, we used nuclear magnetic resonance (NMR) spectroscopy to determine the structure of the free enzyme. MerB is characterized by a novel protein fold consisting of three noninteracting antiparallel beta-sheets surrounded by six alpha-helices. By comparing the NMR data of free MerB and the MerB/Hg/DTT complex, we identified a set of residues that likely define a Hg/DTT binding site. These residues cluster around two cysteines (C(96) and C(159)) that are crucial to MerB's catalytic activity. A detailed analysis of the structure revealed the presence of an extensive hydrophobic groove adjacent to this Hg/DTT binding site. This extensive hydrophobic groove has the potential to interact with the hydrocarbon moiety of a wide variety of substrates and may explain the broad substrate specificity of MerB.

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Related Citations: 

• 1H, 15N, and 13C resonance assignment of the 23 kDa organomercurial lyase MerB in its free and mercury-bound forms
  Di Lello, P., Benison, G.C., Omichinski, J.G., Legault, P.
  (2004) J Biomol NMR 29: 457

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Organizational Affiliation: 

Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkylmercury lyase	A	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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 55 
• Conformers Submitted: 20 
• Selection Criteria: The submitted models are the 20 structures with no upper bound violation greater that 0.3 armstrongs and no dihedral angle restraint violation greater than 2 degrees and with the lowest energies. 
• OLDERADO: 1S6L Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-25 
• Released Date: 2005-04-19 
Deposition Author(s): Di Lello, P., Benison, G.C., Valafar, H., Pitts, K.E., Summers, A.O., Legault, P., Omichinski, J.G.

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance