Crystal structure of LysZ from Thermus thermophilus with ADP

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus.

Yoshida, A.Tomita, T.Fujimura, T.Nishiyama, C.Kuzuyama, T.Nishiyama, M.

(2015) J Biol Chem 290: 435-447

  • DOI: https://doi.org/10.1074/jbc.M114.595983
  • Primary Citation of Related Structures:  
    3WWL, 3WWM, 3WWN

  • PubMed Abstract: 

    In the biosynthesis of lysine by Thermus thermophilus, the metabolite α-ketoglutarate is converted to the intermediate α-aminoadipate (AAA), which is protected by the 54-amino acid acidic protein LysW. In this study, we determined the crystal structure of LysZ from T. thermophilus (TtLysZ), an amino acid kinase that catalyzes the second step in the AAA to lysine conversion, which was in a complex with LysW at a resolution of 1.85 Å. A crystal analysis coupled with isothermal titration calorimetry of the TtLysZ mutants for TtLysW revealed tight interactions between LysZ and the globular and C-terminal extension domains of the LysW protein, which were mainly attributed to electrostatic forces. These results provided structural evidence for LysW acting as a protecting molecule for the α-amino group of AAA and also as a carrier protein to guarantee better recognition by biosynthetic enzymes for the efficient biosynthesis of lysine.

  • Organizational Affiliation

    From the Biotechnology Research Center, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative acetylglutamate kinase-like protein269Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1541
Find proteins for O50147 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore O50147 
Go to UniProtKB:  O50147
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50147
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.49α = 90
b = 80.49β = 90
c = 152.281γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description