7MOH | pdb_00007moh

Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in complex with 5-diphosphoinositol 1,3,4,6-tetrakisphosphate (5PP-InsP4) and phosphate in conformation B (Pi(B))

• PDB DOI: https://doi.org/10.2210/pdb7MOH/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-05-01 Released: 2022-03-02 
• Deposition Author(s): Wang, H., Shears, S.B.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.148 (Depositor), 0.149 (DCC) 
• R-Value Work: 
  0.117 (Depositor), 0.117 (DCC) 
• R-Value Observed: 
  0.118 (Depositor) 

Literature

A structural expose of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop.

Wang, H., Perera, L., Jork, N., Zong, G., Riley, A.M., Potter, B.V.L., Jessen, H.J., Shears, S.B.

(2022) Nat Commun 13: 2231-2231

• PubMed: 35468885 
• DOI: https://doi.org/10.1038/s41467-022-29673-y
• Primary Citation Related Structures: 
  7MOD, 7MOE, 7MOF, 7MOG, 7MOH, 7MOI, 7MOJ, 7MOK, 7MOL, 7MOM


• PubMed Abstract: 
  

  Structural snapshots of protein/ligand complexes are a prerequisite for gaining atomic level insight into enzymatic reaction mechanisms. An important group of enzymes has been deprived of this analytical privilege: members of the protein tyrosine phosphatase (PTP) superfamily with catalytic WPD-loops lacking the indispensable general-acid/base within a tryptophan-proline-aspartate/glutamate context. Here, we provide the ligand/enzyme crystal complexes for one such PTP outlier: Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1 (AtPFA-DSP1), herein unveiled as a regioselective and efficient phosphatase towards inositol pyrophosphate (PP-InsP) signaling molecules. Although the WPD loop is missing its canonical tripeptide motif, this structural element contributes to catalysis by assisting PP-InsP delivery into the catalytic pocket, for a choreographed exchange with phosphate reaction product. Subsequently, an intramolecular proton donation by PP-InsP substrate is posited to substitute functionally for the absent aspartate/glutamate general-acid. Overall, we expand mechanistic insight into adaptability of the conserved PTP structural elements.

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Organizational Affiliation: 
• Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA. [e-mail].
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
Institute of Organic Chemistry, and CIBSS - the Center for Integrative Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany.
Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.7 kDa 
• Atom Count: 2,891 
• Modeled Residue Count: 308 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase DSP1	A, B	171	Arabidopsis thaliana	Mutation(s): 1  Gene Names: DSP1, PTP135, At1g05000, T7A14.14 EC: 3.1.3.48 (PDB Primary Data), 3.6.1.52 (UniProt)
UniProt
Find proteins for Q9ZVN4 (Arabidopsis thaliana) Explore Q9ZVN4  Go to UniProtKB:  Q9ZVN4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U6J (Subject of Investigation/LOI)	C [auth A], D [auth B]	(1r,2R,3S,4r,5R,6S)-4-hydroxy-2,3,5,6-tetrakis(phosphonooxy)cyclohexyl trihydrogen diphosphate C6 H18 O24 P6 FFZGWHDHUIRNPY-KXXVROSKSA-N
PO4 (Subject of Investigation/LOI)	E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.148 (Depositor), 0.149 (DCC) 
• R-Value Work:  0.117 (Depositor), 0.117 (DCC) 
• R-Value Observed: 0.118 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.129	α = 90
b = 124.129	β = 90
c = 124.129	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Wang, H., Shears, S.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZIAES080046-29

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references
• Version 1.2: 2024-05-22
  Changes: Data collection