1R30

The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme

• PDB DOI: https://doi.org/10.2210/pdb1R30/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-30 Released: 2004-01-13 
• Deposition Author(s): Berkovitch, F., Nicolet, Y., Wan, J.T., Jarrett, J.T., Drennan, C.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.300 
• R-Value Work: 0.256 
• R-Value Observed: 0.256 

Literature

Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.

Berkovitch, F., Nicolet, Y., Wan, J.T., Jarrett, J.T., Drennan, C.L.

(2004) Science 303: 76-79

• PubMed: 14704425 
• DOI: https://doi.org/10.1126/science.1088493
• Primary Citation of Related Structures:  
  1R30


• PubMed Abstract: 
  

  The crystal structure of biotin synthase from Escherichia coli in complex with S-adenosyl-L-methionine and dethiobiotin has been determined to 3.4 angstrom resolution. This structure addresses how "AdoMet radical" or "radical SAM" enzymes use Fe4S4 clusters and S-adenosyl-L-methionine to generate organic radicals. Biotin synthase catalyzes the radical-mediated insertion of sulfur into dethiobiotin to form biotin. The structure places the substrates between the Fe4S4 cluster, essential for radical generation, and the Fe2S2 cluster, postulated to be the source of sulfur, with both clusters in unprecedented coordination environments.

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Organizational Affiliation: 

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.13 kDa 
• Atom Count: 4,982 
• Modelled Residue Count: 625 
• Deposited Residue Count: 738 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin synthase	A, B	369	Escherichia coli	Mutation(s): 0  Gene Names: BIOB EC: 2.8.1.6
UniProt
Find proteins for P12996 (Escherichia coli (strain K12)) Explore P12996  Go to UniProtKB:  P12996

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], H [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4	D [auth A], I [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
DTB	F [auth A], K [auth B]	6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID C10 H18 N2 O3 AUTOLBMXDDTRRT-JGVFFNPUSA-N
FES	E [auth A], J [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
TRS	G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.300 
• R-Value Work: 0.256 
• R-Value Observed: 0.256 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.69	α = 90
b = 155.69	β = 90
c = 90.88	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
Adxv	data processing
XDS	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-13 
Deposition Author(s): Berkovitch, F., Nicolet, Y., Wan, J.T., Jarrett, J.T., Drennan, C.L.

Revision History  

• Version 1.0: 2004-01-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations