2Y3R | pdb_00002y3r

Structure of the tirandamycin-bound FAD-dependent tirandamycin oxidase TamL in P21 space group

• PDB DOI: https://doi.org/10.2210/pdb2Y3R/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces sp. 307-9
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-22 Released: 2011-06-29 
• Deposition Author(s): Carlson, J.C., Li, S., Gunatilleke, S.S., Anzai, Y., Burr, D.A., Podust, L.M., Sherman, D.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Tirandamycin Biosynthesis is Mediated by Co-Dependent Oxidative Enzymes

Carlson, J.C., Li, S., Gunatilleke, S.S., Anzai, Y., Burr, D.A., Podust, L.M., Sherman, D.H.

(2011) Nat Chem 3: 628

• PubMed: 21778983 
• DOI: https://doi.org/10.1038/nchem.1087
• Primary Citation Related Structures: 
  2Y08, 2Y3R, 2Y3S, 2Y4G


• PubMed Abstract: 
  

  Elucidation of natural product biosynthetic pathways provides important insights into the assembly of potent bioactive molecules, and expands access to unique enzymes able to selectively modify complex substrates. Here, we show full reconstitution, in vitro, of an unusual multi-step oxidative cascade for post-assembly-line tailoring of tirandamycin antibiotics. This pathway involves a remarkably versatile and iterative cytochrome P450 monooxygenase (TamI) and a flavin adenine dinucleotide-dependent oxidase (TamL), which act co-dependently through the repeated exchange of substrates. TamI hydroxylates tirandamycin C (TirC) to generate tirandamycin E (TirE), a previously unidentified tirandamycin intermediate. TirE is subsequently oxidized by TamL, giving rise to the ketone of tirandamycin D (TirD), after which a unique exchange back to TamI enables successive epoxidation and hydroxylation to afford, respectively, the final products tirandamycin A (TirA) and tirandamycin B (TirB). Ligand-free, substrate- and product-bound crystal structures of bicovalently flavinylated TamL oxidase reveal a likely mechanism for the C10 oxidation of TirE.

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Organizational Affiliation: 
• Life Sciences Institute and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 238.47 kDa 
• Atom Count: 17,755 
• Modeled Residue Count: 1,962 
• Deposited Residue Count: 2,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TAML	A, B, C, D	530	Streptomyces sp. 307-9	Mutation(s): 0
UniProt
Find proteins for D3Y1I2 (Streptomyces sp. 307-9) Explore D3Y1I2  Go to UniProtKB:  D3Y1I2

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], J [auth B], P [auth C], W [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TIR	F [auth A], Q [auth C]	TIRANDAMYCIN E C22 H29 N O6 ADEAEUKXVJOXIM-YNKBRHJSSA-N
TRK	K [auth B], X [auth D]	TIRANDAMYCIN D C22 H27 N O6 WORJTWSOUPGODS-HYAARBKISA-N
GOL	AA [auth D], H [auth A], M [auth B], N [auth B], S [auth C], T [auth C], Z [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	BA [auth D], CA [auth D], I [auth A], O [auth B], U [auth C], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], L [auth B], R [auth C], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.088	α = 90
b = 106.171	β = 94.63
c = 151.172	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Carlson, J.C., Li, S., Gunatilleke, S.S., Anzai, Y., Burr, D.A., Podust, L.M., Sherman, D.H.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-08-03
  Changes: Database references, Non-polymer description, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary