5GKX | pdb_00005gkx

Crystal structure of TON_0340, apo form

• PDB DOI: https://doi.org/10.2210/pdb5GKX/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Thermococcus onnurineus NA1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-07 Released: 2016-12-14 
• Deposition Author(s): Lee, S.G., Sohn, Y.S., Oh, B.H.
• Funding Organization(s): Ministry of Oceans and Fisheries

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 

Starting Model: experimental

Literature

Identification of a Highly Conserved Hypothetical Protein TON_0340 as a Probable Manganese-Dependent Phosphatase.

Sohn, Y.S., Lee, S.G., Lee, K.H., Ku, B., Shin, H.C., Cha, S.S., Kim, Y.G., Lee, H.S., Kang, S.G., Oh, B.H.

(2016) PLoS One 11: e0167549-e0167549

• PubMed: 27907125 
• DOI: https://doi.org/10.1371/journal.pone.0167549
• Primary Citation Related Structures: 
  5GKX, 5GL2, 5GL3, 5GL4


• PubMed Abstract: 
  

  A hypothetical protein TON_0340 of a Thermococcus species is a protein conserved in a variety of organisms including human. Herein, we present four different crystal structures of TON_0340, leading to the identification of an active-site cavity harboring a metal-binding site composed of six invariant aspartate and glutamate residues that coordinate one to three metal ions. Biochemical and mutational analyses involving many phosphorous compounds show that TON_0340 is a Mn2+-dependent phosphatase. Mg2+ binds to TON_0340 less tightly and activates the phosphatase activity less efficiently than Mn2+. Whereas Ca2+ and Zn2+ are able to bind to the protein, they are unable to activate its enzymatic activity. Since the active-site cavity is small and largely composed of nearly invariant stretches of 11 or 13 amino acids, the physiological substrates of TON_0340 and its homologues are likely to be a small and the same molecule. The Mn2+-bound TON_0340 structure provides a canonical model for the ubiquitously present TON_0340 homologues and lays a strong foundation for the elucidation of their substrate and biological function.

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Organizational Affiliation: 
• Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
Department of Chemistry and Nano Science, Ewha Womans University, Seoul, Korea.
Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea.
Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.78 kDa 
• Atom Count: 4,325 
• Modeled Residue Count: 516 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	259	Thermococcus onnurineus NA1	Mutation(s): 0  Gene Names: TON_0340
UniProt
Find proteins for B6YTD8 (Thermococcus onnurineus (strain NA1)) Explore B6YTD8  Go to UniProtKB:  B6YTD8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.574	α = 90
b = 80.209	β = 90
c = 85.459	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Lee, S.G., Sohn, Y.S., Oh, B.H.

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Funding Organization	Location	Grant Number
Ministry of Oceans and Fisheries	Korea, Republic Of	--

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description