Alkylmercury lyase

 

Mercury is a highly toxic metal. Toxicity can result from three different mercurial forms: elemental, inorganic ion and organomercurial compounds. The ability of bacteria to detoxify mercurial compounds by reduction and volatilisation is conferred by the Mer genes. Organomercurial lyase (MerB), also known as alkylmercury lyase, mediates the first of the two steps in the microbial detoxification of organomercurial salts (the other catalysed by mercuric reductase). It catalyses the protonolysis of the carbon-mercury bond in a wide range of organomercurial salts (primary, secondary, tertiary, alkyl, vinyl, allyl and aryl) to Hg(II) and the respective organic compound [PMID: 10548738]. Hg(II) is subsequently detoxified by mercuric reductase MerA.

 

Reference Protein and Structure

Sequence
P77072 UniProt (4.99.1.2) IPR004927 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli (Bacteria) Uniprot
PDB
1s6l - Solution structure of MerB, the Organomercurial Lyase involved in the bacterial mercury resistance system (solution nmr Å) PDBe PDBsum 1s6l
Catalytic CATH Domains
2.40.10.260 CATHdb (see all for 1s6l)
Click To Show Structure

Enzyme Reaction (EC:4.99.1.2)

primary alkymercury(1+)
CHEBI:83725ChEBI
+
hydron
CHEBI:15378ChEBI
→
alkane
CHEBI:18310ChEBI
+
mercury(2+)
CHEBI:16793ChEBI
Alternative enzyme names: Organomercurial lyase, Organomercury lyase, Alkylmercury mercuric-lyase, Alkylmercury mercuric-lyase (alkane-forming),

Enzyme Mechanism

Introduction

Asp99 activates the first cysteine nucleophile (Cys96). Almost immediately after Cys96 attacks the organomercury compound, coordination of Cys159 occurs with concomitant deprotonation of the attacking thiol by Asp99. The polarised carbon-mercury bond is cleaved and then protonated by the close proximity Asp99, generating an alkane.

Catalytic Residues Roles

UniProt PDB* (1s6l)
Asp99 Asp99A Acts as a general acid/base to activate the cysteine that attacks the mercury. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, activator, increase nucleophilicity, promote heterolysis
Cys96, Cys159 Cys96A, Cys159A Acts as a nucleophile at the mercury centre. Also acts as a general acid/base. covalently attached, hydrogen bond donor, nucleophile, proton donor, activator
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic addition, enzyme-substrate complex formation, intermediate formation, overall reactant used, coordination to a metal ion, coordination, decoordination from a metal ion, intramolecular elimination, overall product formed, enzyme-substrate complex cleavage, native state of enzyme is not regenerated, bond polarisation

References

  1. Lafrance-Vanasse J et al. (2009), J Biol Chem, 284, 938-944. Crystal Structures of the Organomercurial Lyase MerB in Its Free and Mercury-bound Forms: INSIGHTS INTO THE MECHANISM OF METHYLMERCURY DEGRADATION. DOI:10.1074/jbc.m807143200. PMID:19004822.
  2. Wahba HM et al. (2017), J Am Chem Soc, 139, 910-921. 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. DOI:10.1021/jacs.6b11327. PMID:27989130.
  3. Parks JM et al. (2009), J Am Chem Soc, 131, 13278-13285. Mechanism of Hg-C protonolysis in the organomercurial lyase MerB. DOI:10.1021/ja9016123. PMID:19719173.
  4. Di Lello P et al. (2004), Biochemistry, 43, 8322-8332. NMR Structural Studies Reveal a Novel Protein Fold for MerB, the Organomercurial Lyase Involved in the Bacterial Mercury Resistance System†,‡. DOI:10.1021/bi049669z. PMID:15222745.
  5. Benison GC et al. (2004), Biochemistry, 43, 8333-8345. A Stable Mercury-Containing Complex of the Organomercurial Lyase MerB:  Catalysis, Product Release, and Direct Transfer to MerA†. DOI:10.1021/bi049662h. PMID:15222746.

Step 1. Asp99 acts as a general base towards Cys96, activating the thiol for nucleophilic attack at the mercury centre of the organomercury substrate. The increases the coordination number around the metal, has been corroborated by spectroscopic studies [PMID:15222746, PMID:19004822].

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Catalytic Residues Roles

Residue Roles
Cys96A activator, hydrogen bond donor
Asp99A activator, hydrogen bond acceptor, increase nucleophilicity
Cys96A proton donor
Asp99A proton acceptor
Cys96A nucleophile

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, enzyme-substrate complex formation, intermediate formation, overall reactant used, coordination to a metal ion

Step 2. Almost immediately after Cys96 attacks the organomercury compound, coordination to the metal coordinated thiol group by Cys159 occurs with concomitant deprotonation of the attacking thiol by Asp99.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys96A activator, covalently attached
Cys159A activator
Asp99A proton acceptor
Cys159A proton donor, nucleophile

Chemical Components

coordination, proton transfer, decoordination from a metal ion, coordination to a metal ion, intermediate formation, enzyme-substrate complex formation, ingold: bimolecular nucleophilic addition

Step 3. The polarised carbon-mercury bond is cleaved and then protonated by the close proximity Asp99, generating an alkane. The close proximity Asp99 is thought to polarise the C-Hg bond, enhancing its ionic character. Asp99 then acts as the proton donor to a highly anionic character carbon [PMID:19004822]. The mercury remains coordinated by the two cystiene residues, ready to be relayed to MerA to be reduced to the metallic form.

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Catalytic Residues Roles

Residue Roles
Cys96A activator, covalently attached
Asp99A activator, hydrogen bond donor, promote heterolysis
Cys159A activator, covalently attached
Asp99A proton donor

Chemical Components

ingold: intramolecular elimination, proton transfer, overall product formed, enzyme-substrate complex cleavage, native state of enzyme is not regenerated, bond polarisation, decoordination from a metal ion
Download: Image, Marvin File

Step 1. Asp99 acts as a general base towards Cys96, activating the thiol for nucleophilic attack at the mercury centre of the organomercury substrate. The increases the coordination number around the metal, has been corroborated by spectroscopic studies [PMID:15222746, PMID:19004822].

Step 2. Almost immediately after Cys96 attacks the organomercury compound, coordination to the metal coordinated thiol group by Cys159 occurs with concomitant deprotonation of the attacking thiol by Asp99.

Step 3. The polarised carbon-mercury bond is cleaved and then protonated by the close proximity Asp99, generating an alkane. The close proximity Asp99 is thought to polarise the C-Hg bond, enhancing its ionic character. Asp99 then acts as the proton donor to a highly anionic character carbon [PMID:19004822]. The mercury remains coordinated by the two cystiene residues, ready to be relayed to MerA to be reduced to the metallic form.

Products.

Introduction

This alternative mechanism differs from the other proposal in that the departing alkane is protonated by Cys159 on its attack of the Hg, rather than by Asp99.

Catalytic Residues Roles

UniProt PDB* (1s6l)
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic addition, enzyme-substrate complex formation, intermediate formation, overall reactant used, coordination to a metal ion, bimolecular nucleophilic substitution, overall product formed, native state of enzyme is not regenerated, bond polarisation, decoordination from a metal ion

References

Step 1. Asp99 acts as a general base towards Cys96, activating the thiol for nucleophilic attack at the mercury centre of the organomercury substrate. The increases the coordination number around the metal, has been corroborated by spectroscopic studies [PMID:15222746, PMID:19004822].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys96A activator, hydrogen bond donor
Asp99A activator, hydrogen bond acceptor, increase nucleophilicity
Cys96A nucleophile
Asp99A proton acceptor
Cys96A proton donor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, enzyme-substrate complex formation, intermediate formation, overall reactant used, coordination to a metal ion

Step 2. Cys159 attacks Hg, this leads to the alkane dissociating from Hg with the concomitant deprotonation of the attacking thiol by the departing alkane.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys96A activator, covalently attached
Asp99A activator, hydrogen bond donor, promote heterolysis
Cys159A proton donor, nucleophile

Chemical Components

ingold: bimolecular nucleophilic substitution, overall product formed, proton transfer, native state of enzyme is not regenerated, bond polarisation, coordination to a metal ion, decoordination from a metal ion
Download: Image, Marvin File

Step 1. Asp99 acts as a general base towards Cys96, activating the thiol for nucleophilic attack at the mercury centre of the organomercury substrate. The increases the coordination number around the metal, has been corroborated by spectroscopic studies [PMID:15222746, PMID:19004822].

Step 2. Cys159 attacks Hg, this leads to the alkane dissociating from Hg with the concomitant deprotonation of the attacking thiol by the departing alkane.

Products.

Contributors

Sophie T. Williams, Gemma L. Holliday, James Willey