2WSI | pdb_00002wsi

Crystal structure of yeast FAD synthetase (Fad1) in complex with FAD

• PDB DOI: https://doi.org/10.2210/pdb2WSI/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-07 Released: 2010-05-26 
• Deposition Author(s): Leulliot, N., van Tilbeurgh, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.231 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal Structure of Yeast Fad Synthetase (Fad1) in Complex with Fad.

Leulliot, N., Blondeau, K., Keller, J., Ulryck, N., Quevillon-Cheruel, S., Van Tilbeurgh, H.

(2010) J Mol Biology 398: 641

• PubMed: 20359485 
• DOI: https://doi.org/10.1016/j.jmb.2010.03.040
• Primary Citation of Related Structures:  
  2WSI


• PubMed Abstract: 
  

  Flavin adenine dinucleotide (FAD) synthetase is an essential enzyme responsible for the synthesis of FAD by adenylation of riboflavin monophosphate (FMN). We have solved the 1.9 A resolution structure of Fad1, the yeast FAD synthetase, in complex with the FAD product in the active site. The structure of Fad1 shows it to be a member of the PP-ATPase superfamily. Important conformational differences in the two motifs involved in binding the phosphate moieties of FAD compared to the Candida glabrata FMNT ortholog suggests that this loop is dynamic and undergoes substantial conformational changes during its catalytic cycle.

---

Organizational Affiliation: 

Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, CNRS-UMR8619, Université de Paris-Sud, Bât 430, 91405 Orsay Cedex, France.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 36.46 kDa 
• Atom Count: 2,613 
• Modelled Residue Count: 285 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD SYNTHETASE	A	306	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.7.7.2
UniProt
Find proteins for P38913 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38913  Go to UniProtKB:  P38913

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.231 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.871	α = 90
b = 36.861	β = 92.35
c = 79.231	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Leulliot, N., van Tilbeurgh, H.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other