Structural insights into the reduction mechanism of Saccharomyces cerevisia Riboflavin Biosynthesis Reductase Rib7

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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Structural and functional insights into Saccharomyces cerevisiae riboflavin biosynthesis reductase RIB7.

Lv, Z.Sun, J.Liu, Y.

(2013) PLoS One 8: e61249-e61249

  • DOI: https://doi.org/10.1371/journal.pone.0061249
  • Primary Citation of Related Structures:  
    4HA7, 4HA9

  • PubMed Abstract: 

    Saccharomyces cerevisiae RIB7 (ScRIB7) is a potent target for anti-fungal agents because of its involvement in the riboflavin biosynthesis pathway as a NADPH-dependent reductase. However, the catalytic mechanism of riboflavin biosynthesis reductase (RBSRs) is controversial, and enzyme structure information is still lacking in eukaryotes. Here we report the crystal structure of Saccharomyces cerevisiae RIB7 at 2.10 Å resolution and its complex with NADPH at 2.35 Å resolution. ScRIB7 exists as a stable homodimer, and each subunit consists of nine central β-sheets flanked by five helices, resembling the structure of RIB7 homologues. A conserved G(76)-X-G(78)-Xn-G(181)-G(182) motif is present at the NADPH pyrophosphate group binding site. Activity assays confirmed the necessity of Thr79, Asp83, Glu180 and Gly182 for the activity of ScRIB7. Substrate preference of ScRIB7 was altered by mutating one residue (Thr35) to a Lysine, implying that ScRIB7 Thr35 and its corresponding residue, a lysine in bacteria, are important in substrate-specific recognition.

  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
A, B
249Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RIB7YBR153WYBR1203
Find proteins for P33312 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33312 
Go to UniProtKB:  P33312
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33312
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.5α = 90
b = 68.623β = 90
c = 148.954γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references