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: 39.02 kDa 
• Atom Count: 2789 
• Modelled Residue Count: 353 
• Deposited Residue Count: 366 
• Unique protein chains: 1

1R2J

FkbI for Biosynthesis of Methoxymalonyl Extender Unit of Fk520 Polyketide Immunosuppresant

• PDB DOI: 10.2210/pdb1R2J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces hygroscopicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-28 Released: 2003-11-25 
• Deposition Author(s): Watanabe, K., Khosla, C., Stroud, R.M., Tsai, S.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.263 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 

Literature

Crystal Structure of an Acyl-ACP Dehydrogenase from the FK520 Polyketide Biosynthetic Pathway: Insights into Extender Unit Biosynthesis

Watanabe, K., Khosla, C., Stroud, R.M., Tsai, S.-C.

(2003) J Mol Biol 334: 435-444

• PubMed: 14623185 
• DOI: 10.1016/j.jmb.2003.10.021
• Primary Citation of Related Structures:  
  1R2J


• PubMed Abstract: 
  

Polyketide synthases (PKSs) synthesize the polyketide cores of pharmacologically important natural products such as the immunosuppressants FK520 and FK506. Understanding polyketide biosynthesis at atomic resolution could present new opportunities for chemo-enzymatic synthesis of complex molecules. The crystal structure of FkbI, an enzyme involved in the biosynthesis of the methoxymalonyl extender unit of FK520, was solved to 2.1A with an R(crys) of 24.4%. FkbI has a similar fold to acyl-CoA dehydrogenases. Notwithstanding this similarity, the surface and substrate-binding site of FkbI reveal key differences from other acyl-CoA dehydrogenases, suggesting that FkbI may recognize an acyl-ACP substrate rather than an acyl-CoA substrate. This structural observation coincided the genetic experiment done by Carroll et al. J. Am. Chem. Soc., 124 (2002) 4176. Although an in vitro assay for FkbI remains elusive, the structural basis for the substrate specificity of FkbI is analyzed by a combination of sequence comparison, docking simulations and structural analysis. A biochemical mechanism for the role of FkbI in the biosynthesis of methoxymalonyl-ACP is proposed.

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Organizational Affiliation: 

Department of Chemical Engineering, Stanford University, Stanford, CA 94305-5025, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein FkbI	A	366	Streptomyces hygroscopicus	Mutation(s): 0
UniProt
Find proteins for Q9KIE5 (Streptomyces hygroscopicus subsp. ascomyceticus) Explore Q9KIE5  Go to UniProtKB:  Q9KIE5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.263 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.55	α = 90
b = 116.55	β = 90
c = 126.16	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-28 
• Released Date: 2003-11-25 
Deposition Author(s): Watanabe, K., Khosla, C., Stroud, R.M., Tsai, S.-C.

Revision History  

• Version 1.0: 2003-11-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2018-04-04
  Changes: Data collection
• Version 1.5: 2018-04-11
  Changes: Data collection