Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and 3-isopropylmalate

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: experimental
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Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis

Shimizu, T.Yin, L.Yoshida, A.Yokooji, Y.Hachisuka, S.I.Sato, T.Tomita, T.Nishida, H.Atomi, H.Kuzuyama, T.Nishiyama, M.

(2017) Biochem J 474: 105-122

  • DOI: https://doi.org/10.1042/BCJ20160699
  • Primary Citation of Related Structures:  
    5HN3, 5HN4, 5HN5, 5HN6

  • PubMed Abstract: 

    β-Decarboxylating dehydrogenases, which are involved in central metabolism, are considered to have diverged from a common ancestor with broad substrate specificity. In a molecular phylogenetic analysis of 183 β-decarboxylating dehydrogenase homologs from 84 species, TK0280 from Thermococcus kodakarensis was selected as a candidate for an ancestral-type β-decarboxylating dehydrogenase. The biochemical characterization of recombinant TK0280 revealed that the enzyme exhibited dehydrogenase activities toward homoisocitrate, isocitrate, and 3-isopropylmalate, which correspond to key reactions involved in the lysine biosynthetic pathway, tricarboxylic acid cycle, and leucine biosynthetic pathway, respectively. In T. kodakarensis, the growth characteristics of the KUW1 host strain and a TK0280 deletion strain suggested that TK0280 is involved in lysine biosynthesis in this archaeon. On the other hand, gene complementation analyses using Thermus thermophilus as a host revealed that TK0280 functions as both an isocitrate dehydrogenase and homoisocitrate dehydrogenase in this organism, but not as a 3-isopropylmalate dehydrogenase, most probably reflecting its low catalytic efficiency toward 3-isopropylmalate. A crystallographic study on TK0280 binding each substrate indicated that Thr71 and Ser80 played important roles in the recognition of homoisocitrate and isocitrate while the hydrophobic region consisting of Ile82 and Leu83 was responsible for the recognition of 3-isopropylmalate. These analyses also suggested the importance of a water-mediated hydrogen bond network for the stabilization of the β3-α4 loop, including the Thr71 residue, with respect to the promiscuity of the substrate specificity of TK0280.

  • Organizational Affiliation

    Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homoisocitrate dehydrogenase353Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK0280
Find proteins for Q5JFV8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JFV8 
Go to UniProtKB:  Q5JFV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JFV8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.161α = 90
b = 80.161β = 90
c = 142.89γ = 90
Software Package:
Software NamePurpose
Cootmodel building
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-01-04
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description