4GNC

human SMP30/GNL-1,5-AG complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.749 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase

Aizawa, S.Senda, M.Harada, A.Maruyama, N.Ishida, T.Aigaki, T.Ishigami, A.Senda, T.

(2013) Plos One 8: e53706-e53706

  • DOI: 10.1371/journal.pone.0053706
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The senescence marker protein-30 (SMP30), which is also called regucalcin, exhibits gluconolactonase (GNL) activity. Biochemical and biological analyses revealed that SMP30/GNL catalyzes formation of the γ-lactone-ring of L-gulonate in the ascorbic a ...

    The senescence marker protein-30 (SMP30), which is also called regucalcin, exhibits gluconolactonase (GNL) activity. Biochemical and biological analyses revealed that SMP30/GNL catalyzes formation of the γ-lactone-ring of L-gulonate in the ascorbic acid biosynthesis pathway. The molecular basis of the γ-lactone formation, however, remains elusive due to the lack of structural information on SMP30/GNL in complex with its substrate. Here, we report the crystal structures of mouse SMP30/GNL and its complex with xylitol, a substrate analogue, and those with 1,5-anhydro-D-glucitol and D-glucose, product analogues. Comparison of the crystal structure of mouse SMP30/GNL with other related enzymes has revealed unique characteristics of mouse SMP30/GNL. First, the substrate-binding pocket of mouse SMP30/GNL is designed to specifically recognize monosaccharide molecules. The divalent metal ion in the active site and polar residues lining the substrate-binding cavity interact with hydroxyl groups of substrate/product analogues. Second, in mouse SMP30/GNL, a lid loop covering the substrate-binding cavity seems to hamper the binding of L-gulonate in an extended (or all-trans) conformation; L-gulonate seems to bind to the active site in a folded conformation. In contrast, the substrate-binding cavities of the other related enzymes are open to the solvent and do not have a cover. This structural feature of mouse SMP30/GNL seems to facilitate the γ-lactone-ring formation.


    Organizational Affiliation

    Cellular Genetics, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regucalcin
A, B
299Homo sapiensMutation(s): 0 
Gene Names: RGN (SMP30)
Find proteins for Q15493 (Homo sapiens)
Go to Gene View: RGN
Go to UniProtKB:  Q15493
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ASO
Query on ASO

Download SDF File 
Download CCD File 
A, B
1,5-ANHYDROSORBITOL
C6 H12 O5
MPCAJMNYNOGXPB-SLPGGIOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.749 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.407α = 90.00
b = 50.202β = 99.65
c = 86.569γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release