6APX

Crystal structure of human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the monobody YSX1

• PDB DOI: https://doi.org/10.2210/pdb6APX/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12, Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-08-18 Released: 2017-11-01 
• Deposition Author(s): Gumpena, R., Lountos, G.T., Sreejith, R.K., Tropea, J.E., Cherry, S., Waugh, D.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.236 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Literature

Crystal structure of the human dual specificity phosphatase 1 catalytic domain.

Gumpena, R., Lountos, G.T., Raran-Kurussi, S., Tropea, J.E., Cherry, S., Waugh, D.S.

(2018) Protein Sci 27: 561-567

• PubMed: 29052270 
• DOI: https://doi.org/10.1002/pro.3328
• Primary Citation of Related Structures:  
  6APX


• PubMed Abstract: 
  

  The dual specificity phosphatase DUSP1 was the first mitogen activated protein kinase phosphatase (MKP) to be identified. It dephosphorylates conserved tyrosine and threonine residues in the activation loops of mitogen activated protein kinases ERK2, JNK1 and p38-alpha. Here, we report the crystal structure of the human DUSP1 catalytic domain at 2.49 Å resolution. Uniquely, the protein was crystallized as an MBP fusion protein in complex with a monobody that binds to MBP. Sulfate ions occupy the phosphotyrosine and putative phosphothreonine binding sites in the DUSP1 catalytic domain.

---

Organizational Affiliation: 

Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 67.9 kDa 
• Atom Count: 4,658 
• Modelled Residue Count: 602 
• Deposited Residue Count: 616 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1	A	520	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 9  Gene Names: malE, b4034, JW3994, DUSP1, CL100, MKP1, PTPN10, VH1 EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P28562 (Homo sapiens) Explore P28562  Go to UniProtKB:  P28562
PHAROS:  P28562 GTEx:  ENSG00000120129
UniProt Groups	P28562P0AEX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monobody YSX1	B	96	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.236 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.802	α = 90
b = 105.802	β = 90
c = 181.463	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Gumpena, R., Lountos, G.T., Sreejith, R.K., Tropea, J.E., Cherry, S., Waugh, D.S.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references
• Version 1.2: 2018-05-02
  Changes: Data collection, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description