L-fucose isomerase

 

L-fuctose isomerase, also known as arabinose isomerase (EC 5.3.1.3) uses both L-fucose and arabinose as substrates, converting the aldo-hexoses to ketoses to prepare them for aldol cleavage within the L-fucose metabolism pathway.

The enzyme binds the closed form of the sugar and catalyses ring opening to generate a form of open-chain conformation that facilitates the isomerisation reaction, which proceeds via an ene-diol mechanism

 

Reference Protein and Structure

Sequence
P69922 UniProt (5.3.1.3, 5.3.1.25) IPR005763 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1fui - L-FUCOSE ISOMERASE FROM ESCHERICHIA COLI (2.5 Å) PDBe PDBsum 1fui
Catalytic CATH Domains
3.20.14.10 CATHdb 3.40.275.10 CATHdb (see all for 1fui)
Cofactors
Water (1), Manganese(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:5.3.1.25)

L-fucopyranose
CHEBI:2181ChEBI
→
L-fuculose
CHEBI:17617ChEBI
Alternative enzyme names: L-fucose ketol-isomerase,

Enzyme Mechanism

Introduction

Asp361 is thought to act as a general base towards the C1-OH of the cyclic substrate, initiating ring opening. Glu337 then abstracts the alpha proton to the aldehyde group, with concomitant deprotonation of Asp361 by the developing anion, forming an enol intermediate. Asp361 is now charged and acts as a base again but this time at the C2 enol OH, leading to the formation of a ketone group with simultaneous reprotonation of the C1 from Glu337, forming an alpha hydroxyl group. The product cyclises and leaves the active site while a hydroxyl coordinated to the catalytically essential Mn divalent cation deprotonates Asp361, regenerating the active site.

Catalytic Residues Roles

UniProt PDB* (1fui)
Glu337 Glu337A Forms part of the manganese binding site. The residue acts as a general base and acid towards the substrate, facilitating the aldose-ketose interconversion. hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
Asp361 Asp361A Forms part of the manganese bindig site. The residue acts as a general base and acid towards the substrate, initiating ring opening and facilitating the aldose-ketose interconversion hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
His528 His528A Forms part of the manganese 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

proton transfer, bimolecular elimination, decyclisation, assisted keto-enol tautomerisation, intermediate formation, intermediate terminated, native state of enzyme regenerated, inferred reaction step, reaction occurs outside the enzyme, cyclisation

References

  1. Seemann JE et al. (1997), J Mol Biol, 273, 256-268. Structure and mechanism of l-fucose isomerase from Escherichia coli. DOI:10.1006/jmbi.1997.1280. PMID:9367760.
  2. Prabhu P et al. (2010), Appl Environ Microbiol, 76, 1653-1660. Probing the Molecular Determinant for the Catalytic Efficiency of L-Arabinose Isomerase from Bacillus licheniformis. DOI:10.1128/aem.02254-09. PMID:20048061.
  3. Kim JH et al. (2010), Appl Microbiol Biotechnol, 85, 1839-1847. Characterization of an L-arabinose isomerase from Bacillus subtilis. DOI:10.1007/s00253-009-2210-6. PMID:19727704.
  4. Rhimi M et al. (2007), J Bacteriol, 189, 3556-3563. Probing the Essential Catalytic Residues and Substrate Affinity in the Thermoactive Bacillus stearothermophilus US100 L-Arabinose Isomerase by Site-Directed Mutagenesis. DOI:10.1128/jb.01826-06. PMID:17337581.
  5. Collyer CA et al. (1990), Proc Natl Acad Sci U S A, 87, 1362-1366. Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase. DOI:10.1073/pnas.87.4.1362. PMID:2304904.

Step 1. Asp361 deprotonates the C1 alcohol of the sugar, initiating ring-opening. The C5 oxygen deprotonates water.

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Catalytic Residues Roles

Residue Roles
Asp361A hydrogen bond acceptor
Asp361A metal ligand
Glu337A metal ligand
His528A metal ligand
Asp361A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular elimination, decyclisation

Step 2. Glu337 deprotonates the C2 carbon, initiating double bond rearrangement to form the enol-form of the substrate. The newly formed oxyanion deprotonates Asp361.

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Catalytic Residues Roles

Residue Roles
Asp361A hydrogen bond donor
Glu337A hydrogen bond acceptor
Asp361A metal ligand
Glu337A metal ligand
His528A metal ligand
Glu337A proton acceptor
Asp361A proton donor

Chemical Components

proton transfer, assisted keto-enol tautomerisation, intermediate formation

Step 3. Asp361 deprotonates the C2 alcohol, initiating double bond rearrangement, and the C1 atom deprotonates Glu337 to re-form the keto-form of the substrate.

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Catalytic Residues Roles

Residue Roles
Asp361A hydrogen bond acceptor
Glu337A hydrogen bond donor
Asp361A metal ligand
Glu337A metal ligand
His528A metal ligand
Glu337A proton donor
Asp361A proton acceptor

Chemical Components

assisted keto-enol tautomerisation, proton transfer, intermediate terminated

Step 4. In an inferred return step, water deprotonates Asp361 to regenerate the enzyme active site.

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Catalytic Residues Roles

Residue Roles
Asp361A hydrogen bond donor
Asp361A metal ligand
Glu337A metal ligand
His528A metal ligand
Asp361A proton donor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step

Step 5. Ring closing to form the ribulose product is assumed to occur outside of the enzyme active site.

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Catalytic Residues Roles

Residue Roles

Chemical Components

reaction occurs outside the enzyme, cyclisation
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Step 1. Asp361 deprotonates the C1 alcohol of the sugar, initiating ring-opening. The C5 oxygen deprotonates water.

Step 2. Glu337 deprotonates the C2 carbon, initiating double bond rearrangement to form the enol-form of the substrate. The newly formed oxyanion deprotonates Asp361.

Step 3. Asp361 deprotonates the C2 alcohol, initiating double bond rearrangement, and the C1 atom deprotonates Glu337 to re-form the keto-form of the substrate.

Step 4. In an inferred return step, water deprotonates Asp361 to regenerate the enzyme active site.

Step 5. Ring closing to form the ribulose product is assumed to occur outside of the enzyme active site.

Products.

Introduction

The hydride-shift mechanism, in which the hydrogen atom at C2 migrates as a hydride to C1.

Catalytic Residues Roles

UniProt PDB* (1fui)
Glu337, Asp361, His528 Glu337A, Asp361A, His528A Form the manganese 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. Seemann JE et al. (1997), J Mol Biol, 273, 256-268. Structure and mechanism of l-fucose isomerase from Escherichia coli. DOI:10.1006/jmbi.1997.1280. PMID:9367760.

Step 1.

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Catalytic Residues Roles

Residue Roles
Glu337A metal ligand
Asp361A metal ligand
His528A metal ligand

Chemical Components

Step 1.

Contributors

Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, James W. Murray, Craig Porter