5GL4 | pdb_00005gl4

Crystal structure of TON_0340 in complex with Mn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.259 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.214 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea.

Macromolecule Content 

  • Total Structure Weight: 175.58 kDa 
  • Atom Count: 12,366 
  • Modeled Residue Count: 1,590 
  • Deposited Residue Count: 1,614 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C, D, E
A, B, C, D, E, F
269Thermococcus onnurineus NA1Mutation(s): 0 
Gene Names: TON_0340
UniProt
Find proteins for B6YTD8 (Thermococcus onnurineus (strain NA1))
Explore B6YTD8 
Go to UniProtKB:  B6YTD8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YTD8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN

Query on MN



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth D],
P [auth D],
Q [auth D],
R [auth D],
S [auth E],
T [auth E],
U [auth F],
V [auth F],
W [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.259 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.214 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.041α = 90
b = 107.041β = 90
c = 360.961γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Oceans and FisheriesKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description