1R30

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1126/science.1088493

  • 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 c ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Biotin synthase
A, B
369Escherichia coli (strain K12)Gene Names: bioB
EC: 2.8.1.6
Find proteins for P12996 (Escherichia coli (strain K12))
Go to UniProtKB:  P12996
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
DTB
Query on DTB

Download SDF File 
Download CCD File 
A, B
6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID
D-DESTHIOBIOTIN
C10 H18 N2 O3
AUTOLBMXDDTRRT-JGVFFNPUSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
A, B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.256 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 155.690α = 90.00
b = 155.690β = 90.00
c = 90.880γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
XDSdata scaling
SOLVEphasing
Adxvdata processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description