Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.03 kDa 
• Atom Count: 1793 
• Modelled Residue Count: 214 
• Deposited Residue Count: 269 
• Unique protein chains: 1

4M7S

Crystal structure of SeMet BtrN in an OPEN conformation

• PDB DOI: 10.2210/pdb4M7S/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Niallia circulans
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.02 Å
• R-Value Free: 0.218 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

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 U S A 110: 15949-15954

• PubMed: 24048029 
• DOI: 10.1073/pnas.1312228110
• Primary Citation of Related Structures:  
  4M7S, 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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A], C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	F [auth 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: 2.02 Å
• R-Value Free: 0.218 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.408	α = 90
b = 42.058	β = 105.4
c = 50.925	γ = 90

Software Package:

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

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
  Changes: Database references