Biotin synthase

 

Biotin synthase (BioB) is a member of the radical-SAM superfamily. It catalyses the insertion of an S atom between the C6 and C9 carbon atoms of dethiobiotin (DTB). BioB contains [4Fe-4S] clusters involved in the reduction and cleavage of S-adenosyl-L-methionine (AdoMet), generating methionine and a primary 5'-deoxyadenosyl radical responsible for dethiobiotin H-abstraction. i.e. BioB is involved in the activation of AdoMet in the biotin synthesis pathway and the incorporation of S atoms into DTB. An oxygen sensitive Fe/S cluster is bound to each polypeptide chain and is chelated by three catalytic Cys residues. The cluster provides electrons for AdoMet cleavage and can adopt both +1 and +2 redox states.

 

Reference Protein and Structure

Sequence
P12996 UniProt (2.8.1.6) IPR024177 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1r30 - The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme (3.4 Å) PDBe PDBsum 1r30
Catalytic CATH Domains
3.20.20.70 CATHdb (see all for 1r30)
Cofactors
Di-mu-sulfido-diiron(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:2.8.1.6)

thiol group
CHEBI:29917ChEBI
+
S-adenosyl-L-methionine zwitterion
CHEBI:59789ChEBI
+
dethiobiotin(1-)
CHEBI:57861ChEBI
+
di-mu-sulfido-diiron(1+)
CHEBI:33738ChEBI
→
H group
CHEBI:64428ChEBI
+
5'-deoxyadenosine
CHEBI:17319ChEBI
+
L-methionine zwitterion
CHEBI:57844ChEBI
+
biotinate
CHEBI:57586ChEBI
+
di-mu-sulfido-diiron(2+)
CHEBI:33737ChEBI
Alternative enzyme names: Dethiobiotin:sulfur sulfurtransferase,

Enzyme Mechanism

Introduction

Formation of biotin from dethiobiotin (DTB) requires the abstraction of 2 hydrogen atoms from the DTB C6 and C9 carbons. This is carried out by the product of AdoMet reduction, the 5'-deoxyadenosyl radical. Two hydrogen atoms are selectively removed from the C9 methyl and C6 methylene positions of DTB. Radicals of C6 and C9 can then react with sulpur atoms , leading to C-S bond formations at these positions. [4Fe-4S] clusters of +1 oxidation state are required for this process. Since the Fe/S clusters are essential for catalysis, the 3 cluster-chelating Cys residues (Cys 53, Cys 57 and Cys 60) also have a catalytic effect, and are arranged in a conserved C-X3-C-X2-C cysteine triad motif. A fourth cluster ligand, Arg 260 is also essential for catalysis. The +1 iron-sulphur cluster injects one electron into the AdoMet bound in its close proximity. The resulting, unstable suphuranyl radical breaks down into methionine and the 5'-deoxyadenosyl radical. This subsequently abstracts a hydrogen from a specific carbon atom of a glycine residue in the polypeptide chain.

Catalytic Residues Roles

UniProt PDB* (1r30)
Cys53 Cys53(76)A Stabilisation by chelation of the iron-sulphur cluster. metal ligand, electrostatic stabiliser
Cys128, Cys188, Cys97 Cys128(151)A, Cys188(211)A, Cys97(120)A Binds [2Fe-2S] cluster metal ligand
Cys57 Cys57(80)A Stabilisation by chelation of the iron-sulphur cluster. metal ligand, electrostatic stabiliser
Cys60 Cys60(83)A Stabilisation by chelation of the iron-sulphur cluster. metal ligand, electrostatic stabiliser
Arg260 Arg260(283)A The unusual Arg 260 environment is important for preserving charge neutrality within the core by reducing the overall net negative charge of the buried cluster. Arg 260 plays an important role in redox modulation. The Arg 260 side chain can rearrange to bridge the two Fe atoms and facilitate proposed S transfer. alter redox potential, electrostatic stabiliser
*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. Hewitson KS et al. (2002), J Biol Inorg Chem, 7, 83-93. The iron-sulfur center of biotin synthase: site-directed mutants. DOI:10.1007/s007750100268. PMID:11862544.
  2. Vey JL et al. (2011), Chem Rev, 111, 2487-2506. Structural insights into radical generation by the radical SAM superfamily. DOI:10.1021/cr9002616. PMID:21370834.
  3. Taylor AM et al. (2011), Biochemistry, 50, 7953-7963. Reduction of the [2Fe-2S] cluster accompanies formation of the intermediate 9-mercaptodethiobiotin in Escherichia coli biotin synthase. DOI:10.1021/bi201042r. PMID:21859080.
  4. Lotierzo M et al. (2006), Biochemistry, 45, 12274-12281. Biotin synthase mechanism: mutagenesis of the YNHNLD conserved motif. DOI:10.1021/bi060662m. PMID:17014080.
  5. Lotierzo M et al. (2005), Biochem Soc Trans, 33, 820-823. Biotin synthase mechanism: an overview. DOI:10.1042/BST0330820. PMID:16042606.
  6. Jameson GN et al. (2004), Biochemistry, 43, 2022-2031. Role of the [2Fe−2S] Cluster in RecombinantEscherichia coliBiotin Synthase†. DOI:10.1021/bi035666v. PMID:14967042.
  7. Berkovitch F et al. (2004), Science, 303, 76-79. Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme. DOI:10.1126/science.1088493. PMID:14704425.
  8. Ollagnier-de Choudens S et al. (2002), J Biol Chem, 277, 13449-13454. Reductive Cleavage ofS-Adenosylmethionine by Biotin Synthase fromEscherichia coli. DOI:10.1074/jbc.m111324200. PMID:11834738.
  9. Phalip V (1999), Curr Microbiol, 39, 348-350. Cloning of Schizosaccharomyces pombe bio2 by Heterologous Complementation of a Saccharomyces cerevisiae Mutant. DOI:10.1007/s002849900470.
  10. Sanyal I et al. (1994), Biochemistry, 33, 3625-3631. Biotin Synthase: Purification, Characterization as a [2Fe-2S]Cluster Protein, and in vitro Activity of the Escherichia coli bioB Gene Product. DOI:10.1021/bi00178a020.

Step 1.

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Catalytic Residues Roles

Residue Roles
Cys60(83)A electrostatic stabiliser
Cys53(76)A electrostatic stabiliser
Cys57(80)A electrostatic stabiliser
Arg260(283)A electrostatic stabiliser
Cys97(120)A metal ligand
Cys128(151)A metal ligand
Cys188(211)A metal ligand
Cys53(76)A metal ligand
Cys57(80)A metal ligand
Cys60(83)A metal ligand
Arg260(283)A alter redox potential

Chemical Components

Step 1.

Contributors

Emma Penn, Gemma L. Holliday