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: 24.39 kDa 
• Atom Count: 1762 
• Modelled Residue Count: 221 
• Deposited Residue Count: 223 
• Unique protein chains: 1

4XAA

Crystal Structure of AviO1 from Streptomyces viridochromogenes Tue57

• PDB DOI: 10.2210/pdb4XAA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces viridochromogenes Tue57
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-13 Released: 2015-08-05 
• Deposition Author(s): McCulloch, K.M., McCranie, E.K., Sarwar, M., Mathieu, J.L., Gitschlag, B.L., Du, Y., Bachmann, B.O., Iverson, T.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily.

McCulloch, K.M., McCranie, E.K., Smith, J.A., Sarwar, M., Mathieu, J.L., Gitschlag, B.L., Du, Y., Bachmann, B.O., Iverson, T.M.

(2015) Proc Natl Acad Sci U S A 112: 11547-11552

• PubMed: 26240321 
• DOI: 10.1073/pnas.1500964112
• Primary Citation of Related Structures:  
  4XAA, 4XAB, 4XAC, 4XBZ, 4XC9, 4XCA, 4XCB, 4ZPI


• PubMed Abstract: 
  

Orthosomycins are oligosaccharide antibiotics that include avilamycin, everninomicin, and hygromycin B and are hallmarked by a rigidifying interglycosidic spirocyclic ortho-δ-lactone (orthoester) linkage between at least one pair of carbohydrates. A subset of orthosomycins additionally contain a carbohydrate capped by a methylenedioxy bridge. The orthoester linkage is necessary for antibiotic activity but rarely observed in natural products. Orthoester linkage and methylenedioxy bridge biosynthesis require similar oxidative cyclizations adjacent to a sugar ring. We have identified a conserved group of nonheme iron, α-ketoglutarate-dependent oxygenases likely responsible for this chemistry. High-resolution crystal structures of the EvdO1 and EvdO2 oxygenases of everninomicin biosynthesis, the AviO1 oxygenase of avilamycin biosynthesis, and HygX of hygromycin B biosynthesis show how these enzymes accommodate large substrates, a challenge that requires a variation in metal coordination in HygX. Excitingly, the ternary complex of HygX with cosubstrate α-ketoglutarate and putative product hygromycin B identified an orientation of one glycosidic linkage of hygromycin B consistent with metal-catalyzed hydrogen atom abstraction from substrate. These structural results are complemented by gene disruption of the oxygenases evdO1 and evdMO1 from the everninomicin biosynthetic cluster, which demonstrate that functional oxygenase activity is critical for antibiotic production. Our data therefore support a role for these enzymes in the production of key features of the orthosomycin antibiotics.

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Organizational Affiliation: 

Department of Pharmacology, Vanderbilt University, Nashville, TN 37232; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232 [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxygenase	A	223	Streptomyces viridochromogenes Tue57	Mutation(s): 0  Gene Names: aviO1, STVIR_2892
UniProt
Find proteins for Q93KW4 (Streptomyces viridochromogenes Tue57) Explore Q93KW4  Go to UniProtKB:  Q93KW4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.119	α = 90
b = 115.144	β = 90
c = 33.864	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-13 
• Released Date: 2015-08-05 
Deposition Author(s): McCulloch, K.M., McCranie, E.K., Sarwar, M., Mathieu, J.L., Gitschlag, B.L., Du, Y., Bachmann, B.O., Iverson, T.M.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2015-08-19
  Changes: Database references
• Version 1.2: 2015-09-30
  Changes: Database references