Propanediol dehydratase

 

Propanediol dehydratsase, a diol dehydratse (DDH), catalyses the conversion of 1,2-propanediol, glycerol, and 1,2-ethanediol to the corresponding aldehydes via a coenzyme B12 (adenosylcobalamin)-dependent radical mechanism.

It is also dependent on a metal ion, there is still some debate as to whether this is potassium or calcium. QM/MM studies have suggested that Ca(II) is more likely.

 

Reference Protein and Structure

Sequences
Q59470 UniProt (4.2.1.28)
Q59471 UniProt (4.2.1.28)
Q59472 UniProt (4.2.1.28) IPR003206 (Sequence Homologues) (PDB Homologues)
Biological species
Klebsiella oxytoca (Bacteria) Uniprot
PDB
1dio - DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA (2.2 Å) PDBe PDBsum 1dio
Catalytic CATH Domains
3.20.20.350 CATHdb (see all for 1dio)
Cofactors
Potassium(1+) (1), Cob(iii)alamin (1)
Click To Show Structure

Enzyme Reaction (EC:4.2.1.28)

propane-1,2-diol
CHEBI:16997ChEBI
→
propanal
CHEBI:17153ChEBI
+
water
CHEBI:15377ChEBI
Alternative enzyme names: 1,2-propanediol dehydratase, DL-1,2-propanediol hydro-lyase, Adenosylcobalamin-dependent diol dehydratase, Coenzyme B12-dependent diol dehydrase, Diol dehydrase, Diol dehydratase, Dioldehydratase, Meso-2,3-butanediol dehydrase, Propanediol dehydrase, Propane-1,2-diol hydro-lyase,

Enzyme Mechanism

Introduction

The radical mechanism involves binding of 1,2-propanediol to the enzyme to induce homolytic cleavage of the Co-C5' bond of the coenzyme to form cob(II)alamin and the adenosyl radical. Hydrogen abstraction from the substrate follows producing a substrate generated radical and 5'-deoxyadenosine. Rearrangement to the product radical is then followed by abstraction of a hydrogen atom from 5'-deoxyadenosine to produce the hydrated propionaldehyde and regenerate the adenosyl radical. After the Co-C5' bond is reformed and the hydrated aldehyde dehydrated.

Catalytic Residues Roles

UniProt PDB* (1dio)
His143 His143A The migrating hydroxyl group on C2 of substrate is hydrogen-bonded to His143A allowing this residue to assists in the 1,2-hydroxyl group migration and protects radical intermediates. radical stabiliser
Glu170 Glu170A Helps stabilise the transition state for the hydroxyl group migration from C2 to C1 by accepting the proton of the spectator hydroxyl group on C1. It forms part of the potassium binding site. proton shuttle (general acid/base), metal ligand
Asp335 Asp335A Help stabilise the radical intermediates formed during the course of the reaction. It is also involved in the binding of the substrate and intermediates, helping to keep them appropriately oriented and to function as a base in the dehydration of the 1,1-diol intermediate. radical stabiliser
Gln296, Gln141, Glu221, Ser362 Gln296A, Gln141A, Glu221A, Ser362A Form part of the potassium binding site. metal ligand
*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

References

  1. Kawata M et al. (2006), J Biol Chem, 281, 18327-18334. Survey of Catalytic Residues and Essential Roles of Glutamate- 170 and Aspartate- 335 in Coenzyme B12-dependent Diol Dehydratase. DOI:10.1074/jbc.m601910200. PMID:16571729.
  2. Doitomi K et al. (2016), Bull Chem Soc Jpn, 89, 955-964. Computational Mutation Study of the Roles of Catalytic Residues in Coenzyme B12-Dependent Diol Dehydratase. DOI:10.1246/bcsj.20160083.
  3. Liu JZ et al. (2016), Appl Biochem Biotechnol, 179, 1073-1100. Glycerol Dehydratases: Biochemical Structures, Catalytic Mechanisms, and Industrial Applications in 1,3-Propanediol Production by Naturally Occurring and Genetically Engineered Bacterial Strains. DOI:10.1007/s12010-016-2051-6. PMID:27033090.
  4. Doitomi K et al. (2014), Bull Chem Soc Jpn, 87, 950-959. Computational Mutation Design of Diol Dehydratase: Catalytic Ability toward Glycerol beyond the Wild-Type Enzyme. DOI:10.1246/bcsj.20140115.
  5. Yamanishi M et al. (2012), FEBS J, 279, 793-804. Redesign of coenzyme B12 dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols. DOI:10.1111/j.1742-4658.2012.08470.x. PMID:22221669.
  6. Kamachi T et al. (2011), Inorg Chem, 50, 2944-2952. Catalytic Roles of the Metal Ion in the Substrate-Binding Site of Coenzyme B12-Dependent Diol Dehydratase. DOI:10.1021/ic102352b. PMID:21388166.
  7. Toraya T et al. (2010), Biochemistry, 49, 7210-7217. Coenzyme B12-Dependent Diol Dehydratase Is a Potassium Ion-Requiring Calcium Metalloenzyme: Evidence That the Substrate-Coordinated Metal Ion Is Calcium. DOI:10.1021/bi100561m. PMID:20712378.
  8. Kinoshita K et al. (2008), Biochemistry, 47, 3162-3173. Histidine-α143 Assists 1,2-Hydroxyl Group Migration and Protects Radical Intermediates in Coenzyme B12-Dependent Diol Dehydratase†. DOI:10.1021/bi7018095. PMID:18260646.
  9. Schwartz PA et al. (2007), Biochemistry, 46, 7293-7301. Dioldehydrase:  An Essential Role for Potassium Ion in the Homolytic Cleavage of the Cobalt−Carbon Bond in Adenosylcobalamin†. DOI:10.1021/bi700078z. PMID:17516630.
  10. Mansoorabadi SO et al. (2006), Biochemistry, 45, 14362-14370. Analysis of the Cob(II)alamin−5‘-Deoxy-3‘,4‘-anhydroadenosyl Radical Triplet Spin System in the Active Site of Diol Dehydrase†. DOI:10.1021/bi061586q. PMID:17128975.
  11. Shibata N et al. (2003), J Biol Chem, 278, 22717-22725. Structural Rationalization for the Lack of Stereospecificity in Coenzyme B12-dependent Diol Dehydratase. DOI:10.1074/jbc.m301513200. PMID:12684496.
  12. Shibata N et al. (2002), Biochemistry, 41, 12607-12617. Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase. PMID:12379103.
  13. Yamanishi M et al. (2002), Eur J Biochem, 269, 4484-4494. The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol. PMID:12230560.
  14. Masuda J et al. (2000), Structure, 8, 775-788. How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex. PMID:10903944.
  15. Toraya T (2000), Cell Mol Life Sci, 57, 106-127. Radical catalysis of B 12 enzymes: structure, mechanism, inactivation, and reactivation of diol and glycerol dehydratases. DOI:10.1007/s000180050502. PMID:10949584.
  16. Shibata N et al. (1999), Structure, 7, 997-1008. A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase. DOI:10.1016/s0969-2126(99)80126-9. PMID:10467140.

Step 1.

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Catalytic Residues Roles

Residue Roles
Glu170A proton shuttle (general acid/base)
Gln141A metal ligand
Glu170A metal ligand
Glu221A metal ligand
Gln296A metal ligand
Ser362A metal ligand
His143A radical stabiliser
Asp335A radical stabiliser

Chemical Components

Step 1.

Contributors

James W. Murray, Craig Porter, Gemma L. Holliday