3VPS

Structure of a novel NAD dependent-NDP-hexosamine 5,6-dehydratase, TunA, involved in tunicamycin biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb3VPS/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces chartreusis NRRL 3882
• Mutation(s): No 


• Deposited: 2012-03-12 Released: 2012-04-18 
• Deposition Author(s): Wyszynski, F.J., Lee, S.S., Yabe, T., Wang, H., Gomez-Escribano, J.P., Bibb, M.J., Lee, S.J., Davies, G.J., Davis, B.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Biosynthesis of nucleoside antibiotic tunicamycin proceeds via unique exo-glycal intermediates

Wyszynski, F.J., Lee, S.S., Yabe, T., Wang, H., Gomez-Escribano, J.P., Bibb, M.J., Lee, S.J., Davies, G.J., Davis, B.G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.91 kDa 
• Atom Count: 5,003 
• Modelled Residue Count: 604 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent epimerase/dehydratase	A, B	321	Streptomyces chartreusis NRRL 3882	Mutation(s): 0  EC: 4.2.1
UniProt
Find proteins for E5KJ94 (Streptomyces chartreusis) Explore E5KJ94  Go to UniProtKB:  E5KJ94

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
UD1	C [auth A], E [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-CFRASDGPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.453	α = 98.13
b = 51.061	β = 106.65
c = 67.804	γ = 94.36

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Wyszynski, F.J., Lee, S.S., Yabe, T., Wang, H., Gomez-Escribano, J.P., Bibb, M.J., Lee, S.J., Davies, G.J., Davis, B.G.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations