1ZUA

Crystal Structure Of AKR1B10 Complexed With NADP+ And Tolrestat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the high all-trans-retinaldehyde reductase activity of the tumor marker AKR1B10.

Gallego, O.Ruiz, F.X.Ardevol, A.Dominguez, M.Alvarez, R.de Lera, A.R.Rovira, C.Farres, J.Fita, I.Pares, X.

(2007) Proc Natl Acad Sci U S A 104: 20764-20769

  • DOI: 10.1073/pnas.0705659105
  • Primary Citation of Related Structures:  
    1ZUA

  • PubMed Abstract: 
  • AKR1B10 is a human aldo-keto reductase (AKR) found to be elevated in several cancer types and in precancerous lesions. In vitro, AKR1B10 exhibits a much higher retinaldehyde reductase activity than any other human AKR, including AKR1B1 (aldose reductase) ...

    AKR1B10 is a human aldo-keto reductase (AKR) found to be elevated in several cancer types and in precancerous lesions. In vitro, AKR1B10 exhibits a much higher retinaldehyde reductase activity than any other human AKR, including AKR1B1 (aldose reductase). We here demonstrate that AKR1B10 also acts as a retinaldehyde reductase in vivo. This activity may be relevant in controlling the first step of retinoic acid synthesis. Up-regulation of AKR1B10, resulting in retinoic acid depletion, may lead to cellular proliferation. Both in vitro and in vivo activities of AKR1B10 were inhibited by tolrestat, an AKR1B1 inhibitor developed for diabetes treatment. The crystal structure of the ternary complex AKR1B10-NADP(+)-tolrestat was determined at 1.25-A resolution. Molecular dynamics models of AKR1B10 and AKR1B1 with retinaldehyde isomers and site-directed mutagenesis show that subtle differences at the entrance of the retinoid-binding site, especially at position 125, are determinant for the all-trans-retinaldehyde specificity of AKR1B10. Substitutions in the retinaldehyde cyclohexene ring also influence the specificity. These structural features should facilitate the design of specific inhibitors, with potential use in cancer and diabetes treatments.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldo-keto reductase family 1 member B10 X317Homo sapiensMutation(s): 1 
Gene Names: AKR1B10AKR1B11
EC: 1.1.1 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.54 (UniProt)
Find proteins for O60218 (Homo sapiens)
Explore O60218 
Go to UniProtKB:  O60218
NIH Common Fund Data Resources
PHAROS:  O60218
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
X
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
TOL
Query on TOL

Download Ideal Coordinates CCD File 
X
TOLRESTAT
C16 H14 F3 N O3 S
LUBHDINQXIHVLS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TOLKi:  50   nM  BindingDB
TOLIC50:  1.2000000476837158   nM  BindingDB
TOLIC50:  54   nM  BindingDB
TOLIC50:  12   nM  BindingDB
TOLIC50:  10   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.113α = 90
b = 89.113β = 90
c = 78.433γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance