5GOT | pdb_00005got

Crystal structure of SP-PTP, low molecular weight protein tyrosine phosphatase from Streptococcus pyogenes

• PDB DOI: https://doi.org/10.2210/pdb5GOT/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pyogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-29 Released: 2016-09-07 
• Deposition Author(s): Ku, B., Keum, C.W., KIim, S.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal structure of SP-PTP, a low molecular weight protein tyrosine phosphatase from Streptococcus pyogenes

Ku, B., Keum, C.W., Lee, H.S., Yun, H.-Y., Shin, H.-C., Kim, B.Y., Kim, S.J.

(2016) Biochem Biophys Res Commun 478: 1217-1222

• PubMed: 27545603 
• DOI: https://doi.org/10.1016/j.bbrc.2016.08.097
• Primary Citation of Related Structures:  
  5GOT


• PubMed Abstract: 
  

  Streptococcus pyogenes, or Group A Streptococcus (GAS), is a pathogenic bacterium that causes a variety of infectious diseases. The GAS genome encodes one protein tyrosine phosphatase, SP-PTP, which plays an essential role in the replication and virulence maintenance of GAS. Herein, we present the crystal structure of SP-PTP at 1.9 Å resolution. Although SP-PTP has been reported to have dual phosphatase specificity for both phosphorylated tyrosine and serine/threonine, three-dimensional structural analysis showed that SP-PTP shares high similarity with typical low molecular weight protein tyrosine phosphatases (LMWPTPs), which are specific for phosphotyrosine, but not with dual-specificity phosphatases, in overall folding and active site composition. In the dephosphorylation activity test, SP-PTP consistently acted on phosphotyrosine substrates, but not or only minimally on phosphoserine/phosphothreonine substrates. Collectively, our structural and biochemical analyses verified SP-PTP as a canonical tyrosine-specific LMWPTP.

---

Organizational Affiliation: 

Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Bio-Analytical Science, University of Science and Technology, Daejeon, Republic of Korea. Electronic address: [e-mail].

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: 18.15 kDa 
• Atom Count: 1,395 
• Modelled Residue Count: 150 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low molecular weight phosphotyrosine phosphatase family protein	A	153	Streptococcus pyogenes	Mutation(s): 0  Gene Names: ptpA EC: 3.1.3.48
UniProt
Find proteins for Q9A1Y0 (Streptococcus pyogenes serotype M1) Explore Q9A1Y0  Go to UniProtKB:  Q9A1Y0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.003	α = 90
b = 58.003	β = 90
c = 218.229	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Ku, B., Keum, C.W., KIim, S.J.

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations