Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 88.91 kDa 
• Atom Count: 6306 
• Residue Count: 731 
• Unique protein chains: 1

5UL2

Structure of Apo, SeMet-labeled Cobalamin-dependent S-adenosylmethionine radical enzyme OxsB

• DOI: 10.2210/pdb5UL2/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-24 Released: 2017-04-19 
• Deposition Author(s): Bridwell-Rabb, J., Drennan, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.228 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

A B12-dependent radical SAM enzyme involved in oxetanocin A biosynthesis.

Bridwell-Rabb, J., Zhong, A., Sun, H.G., Drennan, C.L., Liu, H.W.

(2017) Nature 544: 322-326

• PubMed: 28346939 
• DOI: 10.1038/nature21689
• Primary Citation of Related Structures:  
  5UL4, 5UL3, 5UL2


• PubMed Abstract: 
  

Oxetanocin A (OXT-A) is a potent antitumour, antiviral and antibacterial compound. Biosynthesis of OXT-A has been linked to a plasmid-borne Bacillus megaterium gene cluster that contains four genes: oxsA, oxsB, oxrA and oxrB. Here we show that both the oxsA and oxsB genes are required for the production of OXT-A. Biochemical analysis of the encoded proteins, a cobalamin (Cbl)-dependent S-adenosylmethionine (AdoMet) radical enzyme, OxsB, and an HD-domain phosphohydrolase, OxsA, reveals that OXT-A is derived from a 2'-deoxyadenosine phosphate in an OxsB-catalysed ring contraction reaction initiated by hydrogen atom abstraction from C2'. Hence, OxsB represents the first biochemically characterized non-methylating Cbl-dependent AdoMet radical enzyme. X-ray analysis of OxsB reveals the fold of a Cbl-dependent AdoMet radical enzyme, a family of enzymes with an estimated 7,000 members. Overall, this work provides a framework for understanding the interplay of AdoMet and Cbl cofactors and expands the catalytic repertoire of Cbl-dependent AdoMet radical enzymes.

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Organizational Affiliation: 

Department of Chemistry, University of Texas, Austin, Texas 78712, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OxsB protein	A	744	Priestia megaterium	Mutation(s): 0  Gene Names: oxsB
Find proteins for O24770 (Bacillus megaterium) Explore O24770  Go to UniProtKB:  O24770

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 2.55 Å
• R-Value Free: 0.228 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.392	α = 90
b = 106.917	β = 90
c = 117.494	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-01-24 
• Released Date: 2017-04-19 
Deposition Author(s): Bridwell-Rabb, J., Drennan, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32-GM108189

Revision History 

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-05-03
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence