2X0K

Crystal structure of modular FAD synthetase from Corynebacterium ammoniagenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Oligomeric State in the Crystal Structure of Modular Fad Synthetase Provides Insights Into its Sequential Catalysis in Prokaryotes

Herguedas, B.Martinez-Julvez, M.Frago, S.Medina, M.Hermoso, J.A.

(2010) J Mol Biol 400: 218

  • DOI: 10.1016/j.jmb.2010.05.018
  • Primary Citation of Related Structures:  
    2X0K

  • PubMed Abstract: 
  • The crystal structure of the modular flavin adenine dinucleotide (FAD) synthetase from Corynebacterium ammoniagenes has been solved at 1.95 A resolution. The structure of C. ammoniagenes FAD synthetase presents two catalytic modules-a C-terminus with ATP-riboflavin kinase activity and an N-terminus with ATP-flavin mononucleotide (FMN) adenylyltransferase activity-that are responsible for the synthesis of FAD from riboflavin in two sequential steps ...

    The crystal structure of the modular flavin adenine dinucleotide (FAD) synthetase from Corynebacterium ammoniagenes has been solved at 1.95 A resolution. The structure of C. ammoniagenes FAD synthetase presents two catalytic modules-a C-terminus with ATP-riboflavin kinase activity and an N-terminus with ATP-flavin mononucleotide (FMN) adenylyltransferase activity-that are responsible for the synthesis of FAD from riboflavin in two sequential steps. In the monomeric structure, the active sites from both modules are placed 40 A away, preventing the direct transfer of the product from the first reaction (FMN) to the second catalytic site, where it acts as substrate. Crystallographic and biophysical studies revealed a hexameric assembly formed by the interaction of two trimers. Each trimer presents a head-tail configuration, with FMN adenylyltransferase and riboflavin kinase modules from different protomers approaching the active sites and allowing the direct transfer of FMN. Experimental results provide molecular-level evidences of the mechanism of the synthesis of FMN and FAD in prokaryotes in which the oligomeric state could be involved in the regulation of the catalytic efficiency of the modular enzyme.


    Organizational Affiliation

    Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBFA, B338Corynebacterium ammoniagenesMutation(s): 0 
Gene Names: ribF
EC: 2.7.1.26 (UniProt), 2.7.7.2 (UniProt)
UniProt
Find proteins for Q59263 (Corynebacterium ammoniagenes)
Explore Q59263 
Go to UniProtKB:  Q59263
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PPV
Query on PPV

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.472α = 90
b = 133.472β = 90
c = 133.472γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance