4HA9

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

• PDB DOI: https://doi.org/10.2210/pdb4HA9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-25 Released: 2013-09-04 
• Deposition Author(s): Lv, Z., Sun, J., Liu, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.265 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

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

Lv, Z., Sun, J., Liu, Y.

(2013) PLoS One 8: e61249-e61249

• PubMed: 23620735 
• 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 55.86 kDa 
• Atom Count: 3,466 
• Modelled Residue Count: 423 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase	A, B	249	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RIB7, YBR153W, YBR1203 EC: 1.1.1.302
UniProt
Find proteins for P33312 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33312  Go to UniProtKB:  P33312

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NDP	Binding MOAD:  4HA9	Ka: 1.50e+4 (M^-1) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.265 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.978	α = 90
b = 68.868	β = 90
c = 150.335	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Lv, Z., Sun, J., Liu, Y.

Revision History  

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