2ZA0

Crystal structure of mouse glyoxalase I complexed with methyl-gerfelin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The identification of an osteoclastogenesis inhibitor through the inhibition of glyoxalase I

Kawatani, M.Okumura, H.Honda, K.Kanoh, N.Muroi, M.Dohmae, N.Takami, M.Kitagawa, M.Futamura, Y.Imoto, M.Osada, H.

(2008) Proc.Natl.Acad.Sci.Usa 105: 11691-11696

  • DOI: 10.1073/pnas.0712239105

  • PubMed Abstract: 
  • Osteoclasts, bone-resorptive multinucleated cells derived from hematopoietic stem cells, are associated with many bone-related diseases, such as osteoporosis. Osteoclast-targeting small-molecule inhibitors are valuable tools for studying osteoclast b ...

    Osteoclasts, bone-resorptive multinucleated cells derived from hematopoietic stem cells, are associated with many bone-related diseases, such as osteoporosis. Osteoclast-targeting small-molecule inhibitors are valuable tools for studying osteoclast biology and for developing antiresorptive agents. Here, we have discovered that methyl-gerfelin (M-GFN), the methyl ester of the natural product gerfelin, suppresses osteoclastogenesis. By using M-GFN-immobilized beads, glyoxalase I (GLO1) was identified as an M-GFN-binding protein. GLO1 knockdown and treatment with an established GLO1 inhibitor in osteoclast progenitor cells interfered with osteoclast generation, suggesting that GLO1 activity is required for osteoclastogenesis. In cells, GLO1 plays a critical role in the detoxification of 2-oxoaldehydes, such as methylglyoxal. M-GFN inhibited the enzymatic activity of GLO1 in vitro and in situ. Furthermore, the cocrystal structure of the GLO1/M-GFN complex revealed the binding mode of M-GFN at the active site of GLO1. These results suggest that M-GFN targets GLO1, resulting in the inhibition of osteoclastogenesis.


    Organizational Affiliation

    Antibiotics Laboratory, Chemical Biology Department, and Biomolecular Characterization Team, Advanced Technology Support Division, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glyoxalase I
A, B
184Mus musculusMutation(s): 0 
Gene Names: Glo1
EC: 4.4.1.5
Find proteins for Q9CPU0 (Mus musculus)
Go to UniProtKB:  Q9CPU0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MGI
Query on MGI

Download SDF File 
Download CCD File 
A
methyl 4-(2,3-dihydroxy-5-methylphenoxy)-2-hydroxy-6-methylbenzoate
methyl-gerfelin
C16 H16 O6
BLXSEOJIXHWXQJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MGIIC50: 230 nM BINDINGMOAD
MGIKi: 230 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.982α = 90.00
b = 65.314β = 101.18
c = 66.159γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
MOLREPphasing
BSSdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance