M-CSA Mechanism and Catalytic Site Atlas

Vanadium-dependent bromoperoxidase (organic sulfide oxidation)

V-BPO, isolated from Ascophyllum nodosum, is a vanadium-dependent haloperoxidase. It catalyses the oxidation of halides by hydrogen peroxide to form hypohalides, which can go on to react with organic substrates in halogenation reactions. In this entry, we show one of the side reactions of the vanadium-dependent haloperoxidases: the oxidation or organic sulfides. V-BPO has the ability to oxidise bromide and, to a lesser extent, chloride and iodide as well as chlorinate organic hydrocarbons. V-BPO contains a vanadium(V) ion with a trigonal bipyramidal coordination sphere. It is coordinated to His486 and a hydroxide in the axial positions, and two oxygen atoms and a hydroxide in the equatorial positions.

Catalyzes the halogenation of organic substrates in the presence of hydrogen peroxide. This entry represents the enzyme's reaction with organic sulfides.

Reference Protein and Structure

Sequence: P81701 (1.11.1.18) (Sequence Homologues) (PDB Homologues)
Biological species: Ascophyllum nodosum (Knotted wrack)
PDB: 1qi9 - X-RAY SIRAS STRUCTURE DETERMINATION OF A VANADIUM-DEPENDENT HALOPEROXIDASE FROM ASCOPHYLLUM NODOSUM AT 2.0 A RESOLUTION (2.05 Å)
Catalytic CATH Domains: 1.10.606.10 (see all for 1qi9)
Cofactors: Vanadate(3-) (1)

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Enzyme Reaction (EC:1.11.1.18)

thioanisole

CHEBI:134281

hydrogen peroxide

CHEBI:16240

→

water

CHEBI:15377

(R)-methyl phenyl sulfoxide

CHEBI:134282

Enzyme reaction links: IntEnz ENZYME ExplorEnz

Alternative enzyme names: Bromoperoxidase, Haloperoxidase, Eosinophil peroxidase,

Enzyme Mechanism

Mechanism Proposal 1 ☆☆☆

Summary
Step 1
Step 2
Step 3
Step 4
Step 5
Step 6
Step 7
Products
All Steps

Introduction

An oxygen of hydrogen peroxide attacks the vanadium centre and causes the elimination of the axial hydroxide, which then deprotonates the bound peroxide to form water. The second oxygen of the peroxide ligand then attacks the vanadium centre and causes the elimination of an equatorial oxygen, which then abstracts the second peroxide proton. This forms a side-on vanadium-peroxo species. The sulfide attacks one of the oxygens of the peroxo group, causing the O-O bond to break and leading to the formation of an axial vanadium-O-sulfide complex. In the final step, the sulfate is eliminated and in an inferred return state a hydroxide deprotonates the histidine activated water to regenerate the cofactor.

Catalytic Residues Roles

UniProt	PDB* (1qi9)
Lys341	Lys341A	Lys341 is thought to polarise the vanadium-bound peroxo group and increase its susceptibility to attack by the sulfide. Lys341 forms a hydrogen bond to His411 and this is thought to modulate its polarising power.	electrostatic stabiliser
His411	His411A	His411 forms a hydrogen bond to Lys341, buffering its polarising power towards the peroxo group.	increase basicity, electrostatic stabiliser, increase acidity
His418	His418A	His418 increases the nucleophilicity of the axial hydroxide, thus making it more able to abstract a proton from hydrogen peroxide	electrostatic stabiliser
Arg349, Gly417 (main-N), Ser416, Arg480	Arg349A, Gly417A (main-N), Ser416A, Arg480A	Forms the positive binding site for the cofactor; activating and stabilising it.	electrostatic stabiliser
His486	His486A	His486 coordinates to the vanadate ion and is thought to be necessary for the formation of the vanadium-peroxo intermediate. It is thought that it is responsible for the lengthening and possible weakening of the axial V-O bond.	activator, metal ligand
Asp490	Asp490A	Helps activate and position the vanadate binding His486.	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, dehydration, acidic bimolecular nucleophilic substitution, intramolecular nucleophilic substitution, bimolecular nucleophilic substitution, unimolecular elimination by the conjugate base, inferred reaction step

References

Dembitsky VM (2003), Tetrahedron, 59, 4701-4720. Oxidation, epoxidation and sulfoxidation reactions catalysed by haloperoxidases. DOI:10.1016/s0040-4020(03)00701-4.
Waller MP et al. (2008), J Phys Chem B, 112, 5813-5823. 51V NMR Chemical Shifts from Quantum-Mechanical/Molecular-Mechanical Models of Vanadium Bromoperoxidase. DOI:10.1021/jp800580n. PMID:18412416.
Zampella G et al. (2005), J Am Chem Soc, 127, 953-960. Reactivity of Peroxo Forms of the Vanadium Haloperoxidase Cofactor. A DFT Investigation. DOI:10.1021/ja046016x. PMID:15656634.
ten Brink HB et al. (2001), Eur J Biochem, 268, 132-138. Sulfoxidation mechanism of vanadium bromoperoxidase fromAscophyllum nodosum. DOI:10.1046/j.1432-1327.2001.01856.x.
Rehder D et al. (2000), J Inorg Biochem, 80, 115-121. Water and bromide in the active center of vanadate-dependent haloperoxidases. DOI:10.1016/s0162-0134(00)00047-7. PMID:10885471.
Littlechild J (1999), Curr Opin Chem Biol, 3, 28-34. Haloperoxidases and their role in biotransformation reactions. DOI:10.1016/s1367-5931(99)80006-4.
Weyand M et al. (1999), J Mol Biol, 293, 595-611. X-ray structure determination of a vanadium-dependent haloperoxidase from Ascophyllum nodosum at 2.0 Å resolution. DOI:10.1006/jmbi.1999.3179. PMID:10543953.
Andersson M et al. (1997), J Org Chem, 62, 8455-8458. Asymmetric Sulfoxidation Catalyzed by a Vanadium-Containing Bromoperoxidase. DOI:10.1021/jo9712456.

Step 1. The axial hydroxide of the vanadate cofactor deprotonates hydrogen peroxide.

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Catalytic Residues Roles

Residue	Roles
His411A	increase basicity
His486A	metal ligand
Asp490A	activator
Lys341A	electrostatic stabiliser
Arg349A	electrostatic stabiliser
His418A	electrostatic stabiliser
His486A	activator
Ser416A	electrostatic stabiliser
Arg480A	electrostatic stabiliser

Chemical Components

proton transfer

Step 2. The activated hydrogen peroxide initiates a nucleophilic attack on the vanadate in a substitution reaction, eliminating water.

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Catalytic Residues Roles

Residue	Roles
His486A	metal ligand
Asp490A	activator
His486A	activator
Lys341A	electrostatic stabiliser
Arg349A	electrostatic stabiliser
His411A	electrostatic stabiliser
Ser416A	electrostatic stabiliser
Gly417A (main-N)	electrostatic stabiliser
His418A	electrostatic stabiliser
Arg480A	electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic addition, dehydration

Step 3. One of the equatorial oxo groups deprotonates the attached hydrogen peroxide.

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Catalytic Residues Roles

Residue	Roles
His486A	metal ligand
Asp490A	activator
His486A	activator
His418A	electrostatic stabiliser
Lys341A	electrostatic stabiliser
Arg349A	electrostatic stabiliser
Ser416A	electrostatic stabiliser
Gly417A (main-N)	electrostatic stabiliser
Arg480A	electrostatic stabiliser

Chemical Components

ingold: acidic bimolecular nucleophilic substitution

Step 4. The peroxide initiates a nucleophilic attack on the vanadate in a substitution reaction, eliminating hydroxide and forming a three membered ring.

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Catalytic Residues Roles

Residue	Roles
His486A	metal ligand
Asp490A	activator
His486A	activator
His411A	electrostatic stabiliser
Lys341A	electrostatic stabiliser
Arg349A	electrostatic stabiliser
Ser416A	electrostatic stabiliser
Gly417A (main-N)	electrostatic stabiliser
Arg480A	electrostatic stabiliser

Chemical Components

ingold: intramolecular nucleophilic substitution

Step 5. The sulfide adds to one of the peroxide oxygen atoms.

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Catalytic Residues Roles

Residue	Roles
His486A	metal ligand
Asp490A	activator
His486A	activator
Lys341A	electrostatic stabiliser
Arg349A	electrostatic stabiliser
Ser416A	electrostatic stabiliser
Gly417A (main-N)	electrostatic stabiliser
His418A	electrostatic stabiliser
Arg480A	electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic substitution

Step 6. The sulfate is eliminated.

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Catalytic Residues Roles

Residue	Roles
His486A	activator, metal ligand
Asp490A	activator
His418A	electrostatic stabiliser
Arg480A	electrostatic stabiliser
Gly417A (main-N)	electrostatic stabiliser
Ser416A	electrostatic stabiliser
Arg349A	electrostatic stabiliser
Lys341A	electrostatic stabiliser

Chemical Components

ingold: unimolecular elimination by the conjugate base

Step 7. Inferred return step to regenerate the cofactor.

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Catalytic Residues Roles

Residue	Roles
His486A	metal ligand
His411A	increase acidity
Lys341A	electrostatic stabiliser
Arg349A	electrostatic stabiliser
Ser416A	electrostatic stabiliser
Arg480A	electrostatic stabiliser
His486A	activator
Asp490A	activator

Chemical Components

inferred reaction step, proton transfer

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Step 1. The axial hydroxide of the vanadate cofactor deprotonates hydrogen peroxide.

Step 2. The activated hydrogen peroxide initiates a nucleophilic attack on the vanadate in a substitution reaction, eliminating water.

Step 3. One of the equatorial oxo groups deprotonates the attached hydrogen peroxide.

Step 4. The peroxide initiates a nucleophilic attack on the vanadate in a substitution reaction, eliminating hydroxide and forming a three membered ring.

Step 5. The sulfide adds to one of the peroxide oxygen atoms.

Step 6. The sulfate is eliminated.

Step 7. Inferred return step to regenerate the cofactor.

Products.

Contributors

Gemma L. Holliday