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Catalytic Site Atlas

CSA LITERATURE entry for 1r30

E.C. namebiotin synthase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 2.8.1.6
CSA Homologues of 1r30
CSA Entries With UniProtID P12996
CSA Entries With EC Number 2.8.1.6
PDBe Entry 1r30
PDBSum Entry 1r30
MACiE Entry 1r30

Literature Report

IntroductionBiotin 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.
MechansimFormation 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.
Reaction

Catalytic Sites for 1r30

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
CysA6060macie:sideChainStabilisation by chelation of the iron-sulphur cluster.
CysA5353macie:sideChainStabilisation by chelation of the iron-sulphur cluster.
CysA5757macie:sideChainStabilisation by chelation of the iron-sulphur cluster.
ArgA260260macie:sideChainThe 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.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
CysB6060macie:sideChainStabilisation by chelation of the iron-sulphur cluster.
CysB5353macie:sideChainStabilisation by chelation of the iron-sulphur cluster.
CysB5757macie:sideChainStabilisation by chelation of the iron-sulphur cluster.
ArgB260260macie:sideChainThe 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.

Literature References

Notes:Site directed mutagenesis studies have also shown that three other cysteine residues (Cys 97, Cys 128 and Cys 188) are important for catalysis. Their exact function is unknown, but it is thought that catalytic dependence on these residues may be to the chelation of a second Fe/S cluster.
Hewitson KS
The iron-sulfur center of biotin synthase: site-directed mutants.
J Biol Inorg Chem 2002 7 83-93
PubMed: 11862544
Ollagnier-de Choudens S
Reductive cleavage of S-adenosylmethionine by biotin synthase from Escherichia coli.
J Biol Chem 2002 277 13449-13454
PubMed: 11834738
Jameson GN
Role of the [2Fe-2S] cluster in recombinant Escherichia coli biotin synthase.
Biochemistry 2004 43 2022-2031
PubMed: 14967042
Berkovitch F
Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.
Science 2004 303 76-79
PubMed: 14704425
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