3ORF

Crystal Structure of Dihydropteridine Reductase from Dictyostelium discoideum

• PDB DOI: https://doi.org/10.2210/pdb3ORF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Dictyostelium discoideum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-07 Released: 2011-07-27 
• Deposition Author(s): Chen, C., Zhuang, N.N., Seo, K.H., Park, Y.S., Lee, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.240 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the dual substrate specificities of mammalian and Dictyostelium dihydropteridine reductases toward two stereoisomers of quinonoid dihydrobiopterin

Chen, C., Kim, H.L., Zhuang, N., Seo, K.H., Park, K.H., Han, C.-D., Park, Y.S., Lee, K.H.

(2011) FEBS Lett 585: 2640-2646

• PubMed: 21819985 
• DOI: https://doi.org/10.1016/j.febslet.2011.07.018
• Primary Citation of Related Structures:  
  3ORF


• PubMed Abstract: 
  

  Up to now, d-threo-tetrahydrobiopterin (DH(4), dictyopterin) was detected only in Dictyostelium discoideum, while the isomer L-erythro-tetrahydrobioterin (BH(4)) is common in mammals. To elucidate the mechanism of DH(4) regeneration by D. discoideum dihydropteridine reductase (DicDHPR), we have determined the crystal structure of DicDHPR complexed with NAD(+) at 2.16 Å resolution. Significant structural differences from mammalian DHPRs are found around the coenzyme binding site, resulting in a higher K(m) value for NADH (K(m)=46.51±0.4 μM) than mammals. In addition, we have found that rat DHPR as well as DicDHPR could bind to both substrates quinonoid-BH(2) and quinonoid-DH(2) by docking calculations and have confirmed their catalytic activity by in vitro assay.

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Organizational Affiliation: 

Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, Republic of Korea.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.05 kDa 
• Atom Count: 7,229 
• Modelled Residue Count: 920 
• Deposited Residue Count: 1,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteridine reductase	A, B, C, D	251	Dictyostelium discoideum	Mutation(s): 0  Gene Names: DDB_G0272684, qdpr EC: 1.5.1.34
UniProt
Find proteins for Q86A17 (Dictyostelium discoideum) Explore Q86A17  Go to UniProtKB:  Q86A17

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.240 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.808	α = 90
b = 129.898	β = 99.99
c = 78.763	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Chen, C., Zhuang, N.N., Seo, K.H., Park, Y.S., Lee, K.H.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2011-10-05
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description