2A59

Structure of 6,7-Dimethyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 5-nitroso-6-ribitylamino-2,4(1H,3H)-pyrimidinedione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Structural basis of charge transfer complex formation by riboflavin bound to 6,7-dimethyl-8-ribityllumazine synthase

Koch, M.Breithaupt, C.Gerhardt, S.Haase, I.Weber, S.Cushman, M.Huber, R.Bacher, A.Fischer, M.

(2004) Eur J Biochem 271: 3208-3214

  • DOI: https://doi.org/10.1111/j.1432-1033.2004.04253.x
  • Primary Citation of Related Structures:  
    2A57, 2A58, 2A59

  • PubMed Abstract: 

    The amino acid residue tryptophan 27 of 6,7-dimethyl-8-ribityllumazine synthase of the yeast Schizosaccharomyces pombe was replaced by tyrosine. The structures of the W27Y mutant protein in complex with riboflavin, the substrate analogue 5-nitroso-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, and the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine, were determined by X-ray crystallography at resolutions of 2.7-2.8 A. Whereas the indole system of W27 forms a coplanar pi-complex with riboflavin, the corresponding phenyl ring in the W27Y mutant establishes only peripheral contact with the heterocyclic ring system of the bound riboflavin. These findings provide an explanation for the absence of the long wavelength shift in optical absorption spectra of riboflavin bound to the mutant enzyme. The structures of the mutants are important tools for the interpretation of the unusual physical properties of riboflavin in complex with lumazine synthase.


  • Organizational Affiliation

    Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6,7-dimethyl-8-ribityllumazine synthase
A, B, C, D, E
159Schizosaccharomyces pombeMutation(s): 1 
Gene Names: rib4
EC: 2.5.1.78
UniProt
Find proteins for Q9UUB1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UUB1 
Go to UniProtKB:  Q9UUB1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUB1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMZ
Query on LMZ

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E]
5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
C9 H14 N4 O7
YMWIHKCBRFEJMH-RPDRRWSUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D],
N [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.15α = 90
b = 144.81β = 90
c = 127.78γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-01-16
    Changes: Structure summary
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-02-14
    Changes: Data collection