5U7B

Crystal structure of a the tin-bound form of MerB formed from Diethyltin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Biochemical Characterization of Organotin and Organolead Compounds Binding to the Organomercurial Lyase MerB Provide New Insights into Its Mechanism of Carbon-Metal Bond Cleavage.

Wahba, H.M.Stevenson, M.J.Mansour, A.Sygusch, J.Wilcox, D.E.Omichinski, J.G.

(2017) J. Am. Chem. Soc. 139: 910-921

  • DOI: 10.1021/jacs.6b11327
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The organomercurial lyase MerB has the unique ability to cleave carbon-Hg bonds, and structural studies indicate that three residues in the active site (C96, D99, and C159 in E. coli MerB) play important roles in the carbon-Hg bond cleavage. However, ...

    The organomercurial lyase MerB has the unique ability to cleave carbon-Hg bonds, and structural studies indicate that three residues in the active site (C96, D99, and C159 in E. coli MerB) play important roles in the carbon-Hg bond cleavage. However, the role of each residue in carbon-metal bond cleavage has not been well-defined. To do so, we have structurally and biophysically characterized the interaction of MerB with a series of organotin and organolead compounds. Studies with two known inhibitors of MerB, dimethyltin (DMT) and triethyltin (TET), reveal that they inhibit by different mechanisms. In both cases the initial binding is to D99, but DMT subsequently binds to C96, which induces a conformation change in the active site. In contrast, diethyltin (DET) is a substrate for MerB and the SnIV product remains bound in the active site in a coordination similar to that of HgII following cleavage of organomercurial compounds. The results with analogous organolead compounds are similar in that trimethyllead (TML) is not cleaved and binds only to D99, whereas diethyllead (DEL) is a substrate and the PbIV product remains bound in the active site. Binding and cleavage is an exothermic reaction, while binding to D99 has negligible net heat flow. These results show that initial binding of organometallic compounds to MerB occurs at D99 followed, in some cases, by cleavage and loss of the organic moieties and binding of the metal ion product to C96, D99, and C159. The N-terminus of MerA is able to extract the bound PbVI but not the bound SnIV. These results suggest that MerB could be utilized for bioremediation applications, but certain organolead and organotin compounds may present an obstacle by inhibiting the enzyme.


    Organizational Affiliation

    Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, Quebec H3C 3J7 Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alkylmercury lyase
A, B
212Escherichia coliMutation(s): 0 
Gene Names: merB
EC: 4.99.1.2
Find proteins for P77072 (Escherichia coli)
Go to UniProtKB:  P77072
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
BR
Query on BR

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Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
ZN6
Query on ZN6

Download SDF File 
Download CCD File 
A, B
Diethyltin dichloride
C4 H10 Cl2 Sn
YFAXVVMIXZAKSR-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.860α = 90.00
b = 88.802β = 97.19
c = 55.010γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)Canada--
National Science Foundation (United States)United States--

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Author supporting evidence, Data collection