3OVP

Crystal Structure of hRPE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.695 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE

Liang, W.G.Ouyang, S.Y.Shaw, N.Joachimiak, A.Zhang, R.G.Liu, Z.J.

(2011) Faseb J. 25: 497-504

  • DOI: 10.1096/fj.10-171207
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The pentose phosphate pathway (PPP) confers protection against oxidative stress by supplying NADPH necessary for the regeneration of glutathione, which detoxifies H(2)O(2) into H(2)O and O(2). RPE functions in the PPP, catalyzing the reversible conve ...

    The pentose phosphate pathway (PPP) confers protection against oxidative stress by supplying NADPH necessary for the regeneration of glutathione, which detoxifies H(2)O(2) into H(2)O and O(2). RPE functions in the PPP, catalyzing the reversible conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate and is an important enzyme for cellular response against oxidative stress. Here, using structural, biochemical, and functional studies, we show that human D-ribulose 5-phosphate 3-epimerase (hRPE) uses Fe(2+) for catalysis. Structures of the binary complexes of hRPE with D-ribulose 5-phosphate and D-xylulose 5-phosphate provide the first detailed molecular insights into the binding mode of physiological ligands and reveal an octahedrally coordinated Fe(2+) ion buried deep inside the active site. Human RPE folds into a typical (β/α)(8) triosephosphate isomerase (TIM) barrel with a loop regulating access to the active site. Two aspartic acids are well positioned to carry out the proton transfers in an acid-base type of reaction mechanism. Interestingly, mutating Ser-10 to alanine almost abolished the enzymatic activity, while L12A and M72A mutations resulted in an almost 50% decrease in the activity. The binary complexes of hRPE reported here will aid in the design of small molecules for modulating the activity of the enzyme and altering flux through the PPP.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribulose-phosphate 3-epimerase
A, B
228Homo sapiensMutation(s): 0 
Gene Names: RPE
EC: 5.1.3.1
Find proteins for Q96AT9 (Homo sapiens)
Go to Gene View: RPE
Go to UniProtKB:  Q96AT9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
XPE
Query on XPE

Download SDF File 
Download CCD File 
A, B
3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
DECAETHYLENE GLYCOL
C20 H42 O11
DTPCFIHYWYONMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.695 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.773α = 90.00
b = 46.758β = 89.97
c = 73.314γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASESphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance