LysX from Thermus thermophilus complexed with AMP-PNP

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus.

Ouchi, T.Tomita, T.Horie, A.Yoshida, A.Takahashi, K.Nishida, H.Lassak, K.Taka, H.Mineki, R.Fujimura, T.Kosono, S.Nishiyama, C.Masui, R.Kuramitsu, S.Albers, S.V.Kuzuyama, T.Nishiyama, M.

(2013) Nat Chem Biol 9: 277-283

  • DOI: https://doi.org/10.1038/nchembio.1200
  • Primary Citation of Related Structures:  
    3VPB, 3VPC, 3VPD

  • PubMed Abstract: 

    LysW has been identified as a carrier protein in the lysine biosynthetic pathway that is active through the conversion of α-aminoadipate (AAA) to lysine. In this study, we found that the hyperthermophilic archaeon, Sulfolobus acidocaldarius, not only biosynthesizes lysine through LysW-mediated protection of AAA but also uses LysW to protect the amino group of glutamate in arginine biosynthesis. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions. The crystal structure of ArgX, the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW, was determined in complex with LysW. Structural comparison and enzymatic characterization using Sulfolobus LysX, Sulfolobus ArgX and Thermus LysX identify the amino acid motif responsible for substrate discrimination between AAA and glutamate. Phylogenetic analysis reveals that gene duplication events at different stages of evolution led to ArgX and LysX.

  • Organizational Affiliation

    Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S6 modification protein
A, B
281Thermus thermophilusMutation(s): 0 
Gene Names: LysXrimK
EC: 6.3.2
Find proteins for Q5SH23 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SH23 
Go to UniProtKB:  Q5SH23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SH23
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.339α = 90
b = 130.339β = 90
c = 77.423γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary