6KY6 | pdb_00006ky6

Crystal structure of a thermostable aldo-keto reductase Tm1743 in complexs with inhibitor epalrestat in space group P3221cc

• PDB DOI: https://doi.org/10.2210/pdb6KY6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-09-16 Released: 2019-10-02 
• Deposition Author(s): Zhang, C.Y., Min, Z.Z., Liu, X.M., Wang, C., Tang, W.R.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.256 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Tolrestat acts atypically as a competitive inhibitor of the thermostable aldo-keto reductase Tm1743 from Thermotoga maritima.

Zhang, C., Min, Z., Liu, X., Wang, C., Wang, Z., Shen, J., Tang, W., Zhang, X., Liu, D., Xu, X.

(2020) FEBS Lett 594: 564-580

• PubMed: 31573681 
• DOI: https://doi.org/10.1002/1873-3468.13630
• Primary Citation Related Structures: 
  6KIK, 6KIY, 6KY6


• PubMed Abstract: 
  

  Tolrestat and epalrestat have been characterized as noncompetitive inhibitors of aldo-ketone reductase 1B1 (AKR1B1), a leading drug target for the treatment of type 2 diabetes complications. However, clinical applications are limited for most AKR1B1 inhibitors due to adverse effects of cross-inhibition with other AKRs. Here, we report an atypical competitive binding and inhibitory effect of tolrestat on the thermostable AKR Tm1743 from Thermotoga maritima. Analysis of the Tm1743 crystal structure in complex with tolrestat alone and epalrestat-NADP ⁺ shows that tolrestat, but not epalrestat, binding triggers dramatic conformational changes in the anionic site and cofactor binding pocket that prevents accommodation of NADP ⁺ . Enzymatic and molecular dynamics simulation analyses further confirm tolrestat as a competitive inhibitor of Tm1743.

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Organizational Affiliation: 
• School of Medicine, Hangzhou Normal University, China.
Institute of Cardiovascular Disease Research, The Affiliated Hospital of Hangzhou Normal University, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 65.11 kDa 
• Atom Count: 4,857 
• Modeled Residue Count: 548 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-diketo-D-gluconic acid reductase	A, B	274	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM_1743, Tmari_1751
UniProt
Find proteins for Q9X265 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X265  Go to UniProtKB:  Q9X265

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	C [auth A], G [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
EPR (Subject of Investigation/LOI)	D [auth A], H [auth B]	{5-[(2E)-2-methyl-3-phenylprop-2-en-1-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl}acetic acid C15 H13 N O3 S2 CHNUOJQWGUIOLD-KEBJEMEDSA-N
CL	E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.256 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.128	α = 90
b = 84.128	β = 90
c = 185.765	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): Zhang, C.Y., Min, Z.Z., Liu, X.M., Wang, C., Tang, W.R.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570738
National Natural Science Foundation of China	China	31870740
National Natural Science Foundation of China	China	31400630

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2020-04-08
  Changes: Database references
• Version 1.2: 2020-05-13
  Changes: Structure summary
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description