5HEE

Crystal structure of the TK2203 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the TK2203 protein from Thermococcus kodakarensis, a putative extradiol dioxygenase

Nishitani, Y.Simons, J.R.Kanai, T.Atomi, H.Miki, K.

(2016) Acta Crystallogr F Struct Biol Commun 72: 427-433

  • DOI: https://doi.org/10.1107/S2053230X16006920
  • Primary Citation of Related Structures:  
    5HEE

  • PubMed Abstract: 

    The TK2203 protein from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (262 residues, 29 kDa) is a putative extradiol dioxygenase catalyzing the cleavage of C-C bonds in catechol derivatives. It contains three metal-binding residues, but has no significant sequence similarity to proteins for which structures have been determined. Here, the first crystal structure of the TK2203 protein was determined at 1.41 Å resolution to investigate its functional role. Structure analysis reveals that this protein shares the same fold and catalytic residues as other extradiol dioxygenases, strongly suggesting the same enzymatic activity. Furthermore, the important region contributing to substrate selectivity is discussed.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein, TK2203 protein
A, B
262Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK2203
UniProt
Find proteins for Q5JHM2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JHM2 
Go to UniProtKB:  Q5JHM2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JHM2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.373α = 90
b = 42.543β = 94.47
c = 143.506γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
SOLVEphasing
RESOLVEphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Ministry of Education, Culture, Sports, Science and Technology of JapanJapan26291012

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations