Aldoxime dehydratase

 

Aldoxime dehydratase (Oxd) is a heme-containing enzyme that catalyses the dehydration of aldoximes (R–CHN–OH) to the corresponding nitrile (R–C'N). Some species of microbes utilise an aldoxime-nitrile pathway, metabolising aldoximes to the corresponding carboxylic acids through nitriles formed by dehydration of aldoximes with aldoxime dehydratase. There are two pathways for the conversion of nitriles to carboxylic acids, i) the hydrolysis of nitriles by nitrilase, and ii) the sequential actions of nitrile hydratase and amidase. Nitriles are important for biological self-defence mechanisms, and are also of interest as intermediates in some industrial processes.

The dehydration reaction proceeds only via N-coordinated substrate in the ferrous heme. The organic substrate is shown by crystallographic and spectroscopic data to be directly coordinated to the heme iron in dehydration of aldoxime, which is a unique example among heme enzymes

 

Reference Protein and Structure

Sequence
Q76K71 UniProt IPR025702 (Sequence Homologues) (PDB Homologues)
Biological species
Rhodococcus erythropolis (Bacteria) Uniprot
PDB
3a15 - Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (OxdRE) (1.79 Å) PDBe PDBsum 3a15
Catalytic CATH Domains
(see all for 3a15)
Cofactors
Heme b (1)
Click To Show Structure

Enzyme Reaction (EC:4.99.1.5)

aliphatic aldoxime
CHEBI:82744ChEBI
→
nitrile
CHEBI:18379ChEBI
+
water
CHEBI:15377ChEBI
Alternative enzyme names: OxdA, Aliphatic aldoxime hydro-lyase,

Enzyme Mechanism

Introduction

It is proposed that the dehydration reaction of the heme-bound aldoxime proceeds in a general acid-base catalysis with His320 working as a catalytic residue in the distal heme pocket. The residue His299 is coordinated as a distal ligand to the Fe(II) centre of the heme prosthetic group, directing the reaction site towards a non-polar region of the active site pocket, while several other residues are implicated in orientating the catalytic acid/base for optimum reactivity.

Catalytic Residues Roles

UniProt PDB* (3a15)
Phe306 Phe306(326)A Phe306 thought to be important for mediating the ratio of hydrophobic and hydrophilic character in the active site, which in turn controls the orientation of the haem and therefore the efficiency of reaction. steric role
His320 His320(340)A Acts as a general acid/base. Correct orientation of His320 known to be crucial for catalytic activity. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, activator, promote heterolysis
His299 His299(319)A heme axial ligand via tele nitrogen. metal ligand, steric role
Glu143, Arg178 Glu143(163)A, Arg178(198)A Form a hydrogen bonding network with HIs320, holding this residue in the correct orientation and activating it to act as a general acid/base. hydrogen bond acceptor, steric role
Ser219 Ser219(239)A Binds the substrate holding it in the correct orientation for the reaction to occur. hydrogen bond acceptor, steric role
*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

intramolecular elimination, proton transfer, radical formation, electron transfer, overall reactant used, cofactor used, overall product formed, native state of enzyme regenerated, native state of cofactor regenerated

References

  1. Sawai H et al. (2009), J Biol Chem, 284, 32089-32096. X-ray crystal structure of michaelis complex of aldoxime dehydratase. DOI:10.1074/jbc.M109.018762. PMID:19740758.
  2. Betke T et al. (2018), Chembiochem, 19, 768-779. Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases. DOI:10.1002/cbic.201700571. PMID:29333684.
  3. Nomura J et al. (2013), Proc Natl Acad Sci U S A, 110, 2810-2815. Crystal structure of aldoxime dehydratase and its catalytic mechanism involved in carbon-nitrogen triple-bond synthesis. DOI:10.1073/pnas.1200338110. PMID:23382199.
  4. Pan XL et al. (2012), J Phys Chem B, 116, 5689-5693. QM/MM study on the catalytic mechanism of heme-containing aliphatic aldoxime dehydratase. DOI:10.1021/jp302114d. PMID:22554192.
  5. Sato H et al. (2010), J Biol Chem, 285, 34793-34802. Novel isonitrile hydratase involved in isonitrile metabolism. DOI:10.1074/jbc.M110.150227. PMID:20826798.
  6. Konishi K et al. (2006), Proc Natl Acad Sci U S A, 103, 564-568. Discovery of a reaction intermediate of aliphatic aldoxime dehydratase involving heme as an active center. DOI:10.1073/pnas.0505412103. PMID:16407114.

Step 1. The Fe(II) centre donates a single electron to the N of the aldoxime, initiating the elimination of water, with concomitant proton abstraction from His320. OxdA reaction is an unusual example of a heme directly activating an organic substrate, unlike the utilization of peroxide or oxygen as a mediator of the catalysis, used by other heme-containing enzymes like P450.

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Catalytic Residues Roles

Residue Roles
Phe306(326)A steric role
Arg178(198)A hydrogen bond donor, steric role
Ser219(239)A hydrogen bond acceptor, steric role
Glu143(163)A hydrogen bond acceptor, steric role
His299(319)A metal ligand, steric role
His320(340)A activator, promote heterolysis, hydrogen bond donor, proton donor

Chemical Components

ingold: intramolecular elimination, proton transfer, radical formation, electron transfer, overall reactant used, cofactor used, overall product formed

Step 2. The Fe(III) centre donates a second single electron to the N of the aldoxime. Spectroscopic studies suggest the Fe metal to adopt an oxidation state like that observed in horse radish peroxidase: a highly oxidised (+4) feryl-oxo heme species [PMID20826798:].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Phe306(326)A steric role
Arg178(198)A hydrogen bond donor, steric role
Ser219(239)A hydrogen bond acceptor, steric role
Glu143(163)A hydrogen bond acceptor, steric role
His299(319)A metal ligand, steric role
His320(340)A hydrogen bond acceptor

Chemical Components

electron transfer, cofactor used

Step 3. His320 abstracts the imine alpha proton, forming a carbon, nitrogen triple bond. The Fe(iV) centre receives two electrons, regenerating the metal centre.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Phe306(326)A steric role
Arg178(198)A hydrogen bond donor, steric role
Ser219(239)A hydrogen bond acceptor, steric role
Glu143(163)A hydrogen bond acceptor, steric role
His299(319)A metal ligand, steric role
His320(340)A activator, hydrogen bond acceptor, proton acceptor

Chemical Components

electron transfer, proton transfer, overall product formed, native state of enzyme regenerated, native state of cofactor regenerated
Download: Image, Marvin File

Step 1. The Fe(II) centre donates a single electron to the N of the aldoxime, initiating the elimination of water, with concomitant proton abstraction from His320. OxdA reaction is an unusual example of a heme directly activating an organic substrate, unlike the utilization of peroxide or oxygen as a mediator of the catalysis, used by other heme-containing enzymes like P450.

Step 2. The Fe(III) centre donates a second single electron to the N of the aldoxime. Spectroscopic studies suggest the Fe metal to adopt an oxidation state like that observed in horse radish peroxidase: a highly oxidised (+4) feryl-oxo heme species [PMID20826798:].

Step 3. His320 abstracts the imine alpha proton, forming a carbon, nitrogen triple bond. The Fe(iV) centre receives two electrons, regenerating the metal centre.

Products.

Contributors

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