Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32032.42 
• Atom Count: 1736 
• Residue Count: 269 
• Unique protein chains: 1

4M7S

Crystal structure of SeMet BtrN in an OPEN conformation

• DOI: 10.2210/pdb4M7S/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Bacillus circulans
• Expression System: Escherichia coli


• Deposited: 2013-08-12 Released: 2013-10-02 
• Deposition Author(s): Goldman, P.J., Drennan, C.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.022 Å
• R-Value Free: 0.218 
• R-Value Work: 0.171 

Literature

X-ray analysis of butirosin biosynthetic enzyme BtrN redefines structural motifs for AdoMet radical chemistry.

Goldman, P.J., Grove, T.L., Booker, S.J., Drennan, C.L.

(2013) Proc.Natl.Acad.Sci.USA 110: 15949-15954

• PubMed: 24048029 
• DOI: 10.1073/pnas.1312228110
• Primary Citation of Related Structures:  
  4M7T


• PubMed Abstract: 
  

The 2-deoxy-scyllo-inosamine (DOIA) dehydrogenases are key enzymes in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics. In contrast to most DOIA dehydrogenases, which are NAD-dependent, the DOIA dehydrogenase from Bacillus circulans (BtrN) is an S-adenosyl-l-methionine (AdoMet) radical enzyme. To examine how BtrN employs AdoMet radical chemistry, we have determined its structure with AdoMet and substrate to 1.56 Å resolution. We find a previously undescribed modification to the core AdoMet radical fold: instead of the canonical (β/α)6 architecture, BtrN displays a (β5/α4) motif. We further find that an auxiliary [4Fe-4S] cluster in BtrN, thought to bind substrate, is instead implicated in substrate-radical oxidation. High structural homology in the auxiliary cluster binding region between BtrN, fellow AdoMet radical dehydrogenase anSME, and molybdenum cofactor biosynthetic enzyme MoaA provides support for the establishment of an AdoMet radical structural motif that is likely common to ~6,400 uncharacterized AdoMet radical enzymes.

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Organizational Affiliation: 

Departments of Chemistry and Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
BtrN	A	269	Bacillus circulans	Mutation(s): 0  Gene Names: btrN EC: 1.1.99.38
Find proteins for Q8G907 (Bacillus circulans) Go to UniProtKB:  Q8G907

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SF4	A	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	A	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.022 Å
• R-Value Free: 0.218 
• R-Value Work: 0.171 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 99.408	α = 90.00
b = 42.058	β = 105.40
c = 50.925	γ = 90.00

Software Package:

Software Name	Purpose
APEX	data collection
PHENIX	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-12 
• Released Date: 2013-10-02 
• Deposition Author(s): Goldman, P.J., Drennan, C.L.

Revision History 

• Version 1.0: 2013-10-02
  Type: Initial release
• Version 1.1: 2014-02-05
  Type: Database references