5JNW | pdb_00005jnw

Crystal structure of bovine low molecular weight protein tyrosine phosphatase (LMPTP) mutant (W49Y N50E) complexed with vanadate and uncompetitive inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5JNW/pdb

• Classification: hydrolase/hydrolase INHIBITOR
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-30 Released: 2017-03-29 
• Deposition Author(s): Stanford, S.M., Aleshin, A.E., Liddington, R.C., Bankston, L., Cadwell, G., Bottini, N.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase.

Stanford, S.M., Aleshin, A.E., Zhang, V., Ardecky, R.J., Hedrick, M.P., Zou, J., Ganji, S.R., Bliss, M.R., Yamamoto, F., Bobkov, A.A., Kiselar, J., Liu, Y., Cadwell, G.W., Khare, S., Yu, J., Barquilla, A., Chung, T.D.Y., Mustelin, T., Schenk, S., Bankston, L.A., Liddington, R.C., Pinkerton, A.B., Bottini, N.

(2017) Nat Chem Biol 13: 624-632

• PubMed: 28346406 
• DOI: https://doi.org/10.1038/nchembio.2344
• Primary Citation Related Structures: 
  5JNR, 5JNS, 5JNT, 5JNU, 5JNV, 5JNW


• PubMed Abstract: 
  

  Obesity-associated insulin resistance plays a central role in type 2 diabetes. As such, tyrosine phosphatases that dephosphorylate the insulin receptor (IR) are potential therapeutic targets. The low-molecular-weight protein tyrosine phosphatase (LMPTP) is a proposed IR phosphatase, yet its role in insulin signaling in vivo has not been defined. Here we show that global and liver-specific LMPTP deletion protects mice from high-fat diet-induced diabetes without affecting body weight. To examine the role of the catalytic activity of LMPTP, we developed a small-molecule inhibitor with a novel uncompetitive mechanism, a unique binding site at the opening of the catalytic pocket, and an exquisite selectivity over other phosphatases. This inhibitor is orally bioavailable, and it increases liver IR phosphorylation in vivo and reverses high-fat diet-induced diabetes. Our findings suggest that LMPTP is a key promoter of insulin resistance and that LMPTP inhibitors would be beneficial for treating type 2 diabetes.

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Organizational Affiliation: 
• Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.
Department of Medicine, University of California, San Diego, La Jolla, California, USA.
Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio, USA.
Institute for Genetic Medicine, University of Southern California, Los Angeles, California, USA.
Department of Respiratory, Inflammation and Autoimmunity, MedImmune LLC, Gaithersburg, Maryland, USA.
Department of Orthopaedic Surgery and Department of Pediatrics, University of California, San Diego, La Jolla, California, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 18.57 kDa 
• Atom Count: 1,501 
• Modeled Residue Count: 154 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low molecular weight phosphotyrosine protein phosphatase	A	159	Bos taurus	Mutation(s): 0  Gene Names: ACP1 EC: 3.1.3.48 (PDB Primary Data), 3.1.3.2 (UniProt)
UniProt
Find proteins for P11064 (Bos taurus) Explore P11064  Go to UniProtKB:  P11064

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6LJ	C [auth A]	2-(4-{[3-(piperidin-1-yl)propyl]amino}quinolin-2-yl)benzonitrile C24 H26 N4 PBIFICWHSUFSCR-UHFFFAOYSA-N
VO4	B [auth A]	VANADATE ION O4 V LSGOVYNHVSXFFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.347	α = 90
b = 125.493	β = 90
c = 45.251	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Stanford, S.M., Aleshin, A.E., Liddington, R.C., Bankston, L., Cadwell, G., Bottini, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK106233

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2017-04-12
  Changes: Database references
• Version 1.2: 2017-05-24
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence, Derived calculations
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description